PERSONAL DATA · National annual award for young scientists of the Spanish Society of Biochemistry...

M.Orozco. Curriculum Vitae

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PERSONAL DATA Name: Modesto Orozco Professional Address: Departament de Bioquímica i Biologia Molecular, Facultat de Química. Universitat de Barcelona. Martí i Franquès 1. Barcelona 08028. SPAIN. Date & place of Birth: October 12th, 1962. Barcelona. SPAIN. Marital Status: Married, 2 children. Passport: SPANISH

EDUCATION Bachelor in Science (Chemistry): Universitat Autónoma de Barcelona. 1985. Highest Qualification. Master in Biochemistry: Universitat Autónoma de Barcelona. 1988. Highest Qualification. Doctor in Philosophy (Chemistry): Universitat Autónoma de Barcelona. 1990. Highest Qualification.


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ACADEMIC POSITIONS Pre-Doctoral research fellow of the Spanish Ministry of Education and Science. Departament de Bioquímica. Universitat de Barcelona. 1987-1989. Assistant Professor of Biochemistry. Departament de Bioquímica. Universitat de Barcelona. 1989-1990. Professor of Biochemistry and Molecular Biology. Departament de Bioquímica. Universitat de Barcelona. 1991-2001. Full Professor of Biochemistry and Molecular Biology. Departament de Bioquímica. Universitat de Barcelona 2002- Principal Scientist. Institut de Recerca Biomèdica. 2004-

SCIENTIFIC POSITIONS Postgraduate Student. Institut Municipal de Investigació Mèdica. Universitat Autònoma de Barcelona. Barcelona. SPAIN. 1986-1987. Postgraduate Student. Departament de Bioquímica. Facultat de Química. Universitat de Barcelona. Barcelona. SPAIN. 1987-1990. Invited Scientist. Biomolecular Structure Unit. The Institute of Cancer Research. Sutton. ENGLAND. 1989. Post-Doctoral Researcher. Departament de Bioquímica. Facultat de Química. Universitat de Barcelona. Barcelona. SPAIN. 1990-1991. Researcher. Departament de Bioquímica. Facultat de Química. Universitat de Barcelona. Barcelona. SPAIN. 1991-. Group Leader. Institut de Recerca Biomèdica. Barcelona Spain, 2003- Associated Researcher. Chemistry Departament. Yale University. Connecticut. USA. 1992-1993.

AWARDS AND HONORS Award of the Spanish Minister of Education and Science for postgraduated students. 1987, 1988 and 1989.

Award for short-term research stances in the foreign. Spanish Minister of Education and Science. 1989

Fullbright fellowship. 1992, 1993.

International award of the Chemical Structure Association for young scientists. 1992.

Award of the Spanish Ministry for excellence in teaching in the period 1987-1992.

Award of the Spanish Ministry for excellence in scientific research in the period 1987-1993.

Award of the Spanish Ministry for excellence in scientific research in the period 1994-2000.

Annual award “Sant Albert” of the Catalonian Chemical Association . 1995

National annual award for young scientists “Diaz de Santos”. 1997

National annual award for young scientists of the Spanish Society of Biochemistry (SEBBM). 2000

Distinción Investigadora de la Generalitat de Catalunya. 2000.

FEBS Anniversary Prize of the Gesellschaft für Biochemie und Molekularbiologie. 2001.

Annual Brucker Research Award from the Spanish Society of Biophysics. 2010

Fellow of the Fundación Emilio Botin. 2007-

ERC Advanced Fellow. 2011-2015


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EXTERNAL GRANT SUPPORT Grant QFN89-4001 of the CIRIT. "Design of drugs with agonist and antagonist activity against the A1 and A2 receptors of adenosine. 1989. Principal Investigator: E.I.Canela. Grant “Molecular Recognition”. CESCA, 1992,1993. Amount 3.000.000 UC (ptas). Principal Investigator: M.Orozco. Grant PM92-0055-CO2-01. “Diseño de nuevas estrategias para el modelado de sistemas bioquímicos y farmacológicos”. 1992. Principal Investigator: F.J.Luque. Grant “Uso de supercomputarores para el estudio de sistemas bioquímicos”. CESCA, 1994. Amount 12.000.000 UC (ptas). Principal Investigator: M.Orozco. Grant PB93-0779 de la DGYCIT. “Desarrollo de nuevos métodos para la simulación del DNA. Aplicación en ele studio de la estructura y susceptibilidad a drogas del DNA”. 1994-1996. Amount: 8.800.000 ptas. Principal Investigator: M.Orozco. Excellence Network “Quimica Teórica” subvencionada por la Generalitat de Catalunya. Amount: 1.500.000 ptas. Coordinator: R. Carbó. 1994 Excellence Network “Quimica Teórica” subvencionada por la Generalitat de Catalunya. Amount: 900.000 ptas. Coordinator: R. Caballol. 1995 Excellence Network ”Modelització de molecules bioactives” subvencionada por la Generalitat de Catalunya. Amount: 1.300.000. Principal Investigator M.Orozco. 1995, 1997 Grant del Centro de Supercomputación de Cataluña CESCA: “Uso de supercomputarores para el estudio de sistemas bioquímicos”. 1995-96. Amount 13.000.000 UC (ptas). Principal Investigator: M.Orozco. Grant for consolidated reserach Groups. Generalitat de Catalunya (1995SGR 00274). Amount: 1.300.000 ptas. Principal Investigator: M.Orozco. Grant from the Ministry of Education and Science for the organization of the Workshop on Molecular Modeling of Solvation in Biochemical systems (CO94-0764). Amount 400.000 ptas. Principal Investigator: M.Orozco. Europena Grant: “Structural studies on the mechanism of DNA excision repair (BIO4-CT96-0509)”. Amount 103.000 ECUS. Principal Investigator: M.Orozco. Support action for European Grants “Structural studies on the mechanism of DNA excision repair” (BIO96-2385-CE). Amount 1360000 ptas. Principal Investigator: M.Orozco.


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Biomedica Resarch Grant “Role of counterions in tetraplex structure and stability”. Financiado por Wellcome Trust (049478/Z/96/Z/JPS/JMW/CG). Amount 8.220 UK £. Principal Investigator. Charles A. Laughton. Supercomputer Grant, Universitat de Barcelona, Fundació Catalana per la Recerca y CESCA. “Reconocimiento molecular en sistemas bioquímicos”. Amount 800.000 ptas. Principal Investigator: M.Orozco. Grant from the Spanish Minstry of Science. “Simulación de formas inusuales del DNA. Implicaciones funcionales en el diseño de nuevas terapias”. Amount 14.000.000 ptas (PB96-1005). Principal Investigator: M.Orozco Grant Fundació La Marató de TV3-97. “Diseño de nuevos fármacos inhibidores de la acetilcolinesterasa para el tratamiento del Alzheimer”. Amount 23.850.000 ptas. Principal Investigator: P.Camps. Grant NATO para investigación sobre la estructura de triples hélices de DNA. Grant colaboración con Inglaterra y Estados Unidos. Cuantia 4000 UK £.. Principal Investigator: C.Laughton. Coordinador of the excellence network ”modelització de molecules bioactives” subvencionada por la Generalitat de Catalunya. 1997XT 00026. Amount: 1.400.000. Principal Investigator M.Orozco. 1997 Consolidated Group from the Universitat de Barcelona. Subvención de la UB. Amount 800.000. Principal Investigator M.Orozco. 1998-99. European Grant. “Structural studies of bacterial, viral and cellular kinases of medical interest”. BIO-CT-98-0354. Principal Investigator M.Orozco. Amount 19920000. 1999-2000. Grups de Recerca Consolidats. 1999SGR00324. Generalitat de Catalunya. Principal Investigator M.Orozco. Amount 1500000. 2000-2001. Acciones integradas Hispano-Británica. Grant “Estudio de formas inusuales del DNA de potencial utilidad terapéutica”. Principal Investigator M.Orozco. Amount 129000. 2000-2001. Grant for collaborative actions with companies. DURSI-Generalitat de Catalunya. “Desarrollo de metodologías para la representación de efectos de solvente en el diseño de fármacos”. Principal Investigator M.Orozco. 2001-2002. Amount 3750000 ptas European Grant “Structural studies on the mechanism of DNA excision repair. Grant Europeo. QLG1-CT-1999-0008”. Principal Investigator M.Orozco. Amount 29289280 ptas. 2000-2003.


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Grant “Estudio teórico de formas inusuales del DNA. Implicaciones en el diseño de nuevas terapias”. Spanish Ministry of Science. Principal Investigator M.Orozco. Amount 15000000. 2000-2003. Excellent Network of Bioinformatics. Red Catalana Bioinformatica. Direcció General de Recerca. Principal Investigator M.Orozco. Amount 1400000 ptas. 2002-2003. Consolidated Research Groups. 2001SGR. Generalitat de Catalunya. Principal Investigator M.Orozco. Amount 3300000 ptas. 2002-2004. Grant from the Ramón Areces Foundation. “Estudios Bioinformaticos de las mutaciones patológicas”. Principal Investigator M.Orozco. Amount 72000 Euros. Excellence Network on Bioinformatics. Generalitat de Catalunya. Principal Investigator M.Orozco. Amount 8000 Euros 2003-2004. Grant “Simulaciones Teoricas de formas inusuales del DNA. Implicaciones biotecnológicas y biomédicas”. BIO2003-06848. Ministerio de Ciencia y Tecnología. Plan Nacional de Biotecnología. Principal Investigator M.Orozco. Amount 285500 Euros. 2004-2006. Grant. “Design of new oligonucleotide-based antigene and antisensetherapies”. Fundación BBVA. Accion especial de Bioinformatica. Principal Investigator M.Orozco. Amount 70000 Euros. 2004-2006 “Structural bioinformatics node- GNV4”. National Institute of Bioinformatics. Principal Investigator M.Orozco. Amount 270.630,58 Euros. 2004-2007 EUGINDAT- European Genomics Initiative on Disorders of plasma membrana Imino acid Transporters. European Union. Principal Investigator M.Orozco. Amount 92.067,00 Euros. 2004-2007 Grant “Bioinformática y modelización en Genómica Estructural”. National Institute of Bioinformaics GEN2003-20642-C09-07. Principal Investigator M.Orozco. Amount 114.000 Euros. 2004-2007 Grant “Estudio de formas inusuales o tensionadas del DNA. Implicaciones biotecnológicas y biomédicas”. BIO2006-01602 Ministerio Educación y Ciencia. Principal Investigator M.Orozco. Amount 387.563 Euros. 2006-2009. Grant for consolidated reserach Group. Generalitat de Catalunya. 2005SGR00286. Principal Investigator M.Orozco. Amount 49600 Euros. 2006-2009 Support activities “Expanding the frontiers of Molecular Dynamics Simulations”. BIO2009-06316-E. Ministry of Science and Innovation. Principal Investigator M.Orozco. Amount 10.000 Euros. 2009.


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Support activities. “Expanding de frontiers os Molecular Dynamics Simulations“. ARCS2009-00168. Generalitat de Catalunya (AGAUR). Principal Investigator M.Orozco. Amount 5.000 Euros. 2009. Excellence “Biología Computacional en el diseño de biomoléculas”. Fundación Marcelino Botin. Principal Investigator M.Orozco. Amount. 880.000 Euros 2007-2012. Consolided Group “Modelització Molecular i Bioinformática”. 2009 SGR 1348. Generalitat de Catalunya (AGAUR) Principal Investigator M.Orozco. Amount 79.040 Euros. 2009-2013 Grant “Red Temática de Investigación cooperativa en Biomedicina Computacional COMBIOMED-RD07-0067/0009. Instituto de Salud Carlos III. Principal Investigator M.Orozco. Amount 196.000 Euros. 2007-2011 Structural Bioinformatics Node GNV4. National Institute of Bioinformatics. Genoma España. Ministerio de Ciencia e Innovación. Principal Investigator M.Orozco. Amount 99.685 Euros. 2007-2010. Excellence network Grnt “Convenio de colaboración para el desarrollo del programa de actividad investigadora del equipo de investigación en materia de supercomputación y eCiencia” CONSOLIDER. Principal Investigator M.Orozco. Amount 333.335,00 Euros 2008-2012. Research Project EC Marie Curie- Manuel Rueda. “Incorporating flexibility into protein-ligand Docking”. Principal Investigator M.Orozco. Amount 221.673,82 Euros. 2009-2012 Grant “Simulaciones de formas inusuales o tensionadas de los ácidos nucleicos de potenciál interés biotecnológico y biomédico”. Spanish Ministry of Science. BIO2009-10964. Principal Investigator M.Orozco. Amount 385.000,00 Euros. 2009-2012. Support grant “Exascale Challenges in Computational Biology”. ARCS 2010-00277. Generalitat de Catalunya (AGAUR). Principal Investigator M.Orozco Amount 6.000 Euros. 2010 Support Grant “Exascale Challenges in Computational Biology” BIO2010-11049-E. Ministerio de Ciencia e Innovación. Principal Investigator M.Orozco. Amount 8.000 Euros. 2011 Grant “Desarrollo de nuevas etiquetas peptídicas (EpiTag)”.INNPACTO IPT-010000-2010-019.Ministerio de Ciencia e Innovación. Principal Investigator M.Orozco. Amount 153.916 Euros. 2010-2012 Grant “Scalable Software Services for Life Science”. ScalaLife. European Commission. Principal Investigator M.Orozco. Amount 259.487 Euros. 2010-2013.


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Maire Curie project FP7-2010-IIF-275996 “Epigenetic control of Chromatin Structure-Solving and intertwined puzzle with a Specialized coarse-grained model”. Principal Investigator M.Orozco. Amount 174.380,80 Euros. 2011-2013 European Research Council. Advanced Grant. “DIMSIM. Multiscale simulation of DNA”. Euros. Principal Investigator M.Orozco. Amount 1.961.400. 2011-2015


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SCIENTIFIC AREAS OF INTEREST Our long term goal is the understanding of Biological Systems in terms of basic physical principles described by means of the basic formalisms of computacional chemistry. Within this general interest we are working in three main directions: i) Developement of methods for the study of molecular interactions, ii) Study of macromolecular dynamics, and iii) Study of nucleic acids structure and function. In practical terms, our work has been crystallized in Development of new methods for the study of molecular interactions. Here our work has been focussed in the development of new algorithms for a more accurate treatment of molecular interactions. Of special interest are the works devoted to the improvement in the representation of solvent effects (Forti et al., J.Comput.Chem., 2007; Bidon-Chanal et al., TCA, 2009; Klamtz et al., Acc.Chem.Res., 2009, Soteras et al., JCAMD., 2010) and highly polarized systems (Soteras et al., JCTC., 2007); Soteras et al., PCCP, 2008). Several of the developed methods have been succesfully applied to study a wide range of chemical systems (Blas et al., Chem.Eur.J., 2007; Soliva et al., J.Med.Chem., 2007; Fort et al., J.Biol.Chem., 2007, Garcia-Fandiño et al., J.Am.Chem.Soc., 2009; Kowalcyk et al., Proc. Natl. Acad. Sci. USA, 2010). Recently, in collaboration with colleagues at Minnessota we have developed a new QM framework for the MD analysis of macromolecules, a method that we are now refining (Xie et al., JCTC., 2009).

Development of methods for the high througput study of dynamics in macromolecules The development of new supercomputers, such as Mare Nostrum is changing the paradigm of use of molecular dynamics, which in a very near future will become techniques used in a massive way by non-expert users, wich will expect the equivalent to a time-dependent PDB database. In this area our major contributions are organized around the MODEL project (Molecular Dynamics Extended Library; Rueda et al., PNAS, 2007; Carrillo & Orozco Proteins 2008, Rueda et al., Structure 2007, Laughton et al., Proteins 2009, Emperador et al., Biophys.J. 2008, Meyer et al., Structure 2009, Emperador et al., J.Chem.Theor.Comput., 2008, Cozzini et al., J.Med.Chem., 2008, Raimondi et al., PLOS CB 2010,, Stein et al., Structure 2010), a very agreesive innitiative that has provided already the first tools for the HT preparation, execution and processing of MD simulations.

Development of Coarse Grained Methods for the study of protein dynamics. In the last years and related to our MODEL project we have been much attracted by coarse-grained methods, with special emphasis in method development. We have explored several coarse grained approaches, including: Normal Mode Analysis (Rueda et al., Structure 2007, Camps et al., Bioinformatics 2009, Emperador et al., Proteins, 2009, Orellana et al., JCTC 2010), Brownian Dynamics (Carrillo & Orozco Proteins 2008, Emperador et al., Biophys,J, 2008, Camps et al., Bioinformatics 2009). Discrete Molecular Dynamics (Emperador et al., J.Chem.Theor.Comput. 2008, Biophys,J, 2008, Emperador et al., Proteins 2009).

Study of inusual or stressed forms of DNA. This has been for many years the central topic of research in the group. The development of the PARMBSC0 force-field (a refinement of parm99) in 2007 (Pérez et al., Biophys J., 2007; paper with 261 citations in 4 years; reviewed in Orozco et al., Curr.Opin.Struct.Biol., 2008 & Pérez et al. Acc.Chem.Res. 2011) was instrumental to the simulation of DNA, allowing us to study for the first time large conformational transitions, including B��A conformational changes (Noy et al., Nucl. Acids Res., 2007), chemical induced unfolding (Pérez & Orozco, Angew. Chem.Int.Ed.Eng., 2010) and hairping folding (Portella & Orozco, Angew. Chem.Int.Ed.Eng., 2010). Using this new force-field we were also able to study a variety of inusual DNA structures, including hybrids (Noy et al., J.Am.Chem.Soc. 2008; Watts et al., Nuc.Acids Res., 2010), PNAS (Ortega et al., Org.Lett., 2007), naphto-DNAs (Vázquez et al.,


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J.Phys.Chem.B., 2008), quadruplexes (Gross et al., Chem.Com., 2008), LNA (Saneyoshi et al., Nucl.Acids Res., 2009), or DNA containing mutated bases (Faustino et al., J.Am.Chem.Soc., 2009). More interestingly, PARMBSC0 combined with supercomputer resources allowed, for the first time, to obtain nearly converged pictures of DNA flexibility (Pérez et al., J.Am.Chem.Soc., 2007; Portella & Orozco, Angew. Chem.Int.Ed.Eng., 2010, Pérez et al., Angew.Chem.Int.Ed.Eng., 2010), from which mesoscopic descriptors of DNA and RNA flexibility can be obtained (Pérez et al., Nucleic Acids Res., 2008; Faustino et al., Biophys J., 2010; Lavery et al., Nucleic Acids Res., 2010).

Conexión between physical properties and biological functionality of nucleic acids. Using mesoscopic descriptors of DNA flexibility (see above) we have determined the existence of a tight conection between inusual physical properties and key regulatory regions (Goñi et al., Genome Biol., 2007, Highly accessed paper; Goñi et al., Bioinformatics 2008; Deniz et al., BMC Genomics 2011 Puente et al., Nature 2011). At present time we are exploring, with the help of our recently developed experimental facilities, whether these descriptors can help to understand a potential connection between physical properties, chromatin structure, epigenetic signatures and gene regulation mechanisms (Pérez et al., submitted) .

THESIS SUPERVISION

Carlos Alemán. Honor Thesis. “Estrategias para la parametrización de campos de fuerza a partir de cálculos

mecanocuánticos”. Universitat de Barcelona. 1990.

Cristobal Alhambra. Doctoral Thesis. “Aproximaciones teóricas para el estudio del reconocimiento molecular

de nucleótidos y ácidos nucleicos”. Universitat de Barcelona. 1996.

Xavier Barril. Master Thesis. “Interaccions per pont salí: estabilitat dels complexes neutres i iònic en fase gas,

en solució i en les proteines”. Universitat de Barcelona. 1997.

Elena Cubero. Master Thesis. “Estudi teòric de la isomeria azido-tetrazol: efectes del solvent i dels

substituents, i mecanisme d’isomerització”. Universitat de Barcelona. 1997

Joaquin Lizondo. Honor Thesis. “Análisis estructural por dinámica molecular del péptido cíclico

CYSIGSRC” Universitat de Barcelona. 1997

Carles Colominas. Doctoral Thesis “Modelos teóricos para el estudio de sistemas químicos en solución”.

Institut Químic de Sarria. 1999

Carles Eduard Curutchet. Master Thesis. “Solvatació en n-octanol. Parametrització del model continu MST”.

Universitat de Barcelona. 2001.

Manuel Rueda. Master Thesis. “L’efecte de la tautomeria i dels grups amino remots en la interacció per ponts

d’hidrogen. Un estudi teòric”. Universitat de Barcelona. 2001.

Robert Soliva. Doctoral Thesis. “Estudios teóricos sobre la estructura y el reconocimiento molecular de los

ácidos nucleicos”. Universitat de Barcelona. 2001.

Jordi Muñoz. Master Thesis. “Contribuciones fraccionales a la energía libre de solvatación: aplicación al

diseño de fármacos”. Universitat de Barcelona. 2001.

Carles Ferrer. Master Thesis. “Caracterització de daSAP (disease-associated single amino acid

polimorphisms) en termes de propietats de seqüencia i estructura”. Universitat de Barcelona. 2001.


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Albert Salichs. Master Thesis. “Constants de formació de pont d’hidrogen: parametrització de diverses escales

de pKHB”. Universitat de Barcelona. 2001.

Begoña Hernández. Doctoral Thesis “Estrategias computacionales para el estudio de moléculas bioactivas”.

Universitat de Barcelona 2001.

Xavier Barril. Doctoral Thesis. “Estudis teòrics de mecanismes i especificitat d’interacció lligand-receptor”.


Elena Cubero. Doctoral Thesis. “Estudio teórico de nucleobases: implicaciones estructurales en ácidos

nucleicos”. Universitat de Barcelona 2002.

Carles Curutchet. Doctoral Thesis. “Aplicaciones del método MST a sistemas bioquímicos”. Universitat de

Barcelona 2005.

Carles Ferrer. Doctoral Thesis. “Análisis Bioinformàtica de les mutacions puntuals patològiques”. Universitat

de Barcelona 2005.

Manuel Rueda. . Doctoral Thesis. “Estudio teórico sobre la influencia del solvente en la estructura y dinámica

del DNA”. Universitat de Barcelona 2006.

Ivan Marchán. Master Thesis. “Development of torsional force-field parameters for nucleic acids” Universitat

de Barcelona 2006.

Jose Ramón Blas. Doctoral Thesis. “Dinámica de sistemas de interés biológico. Estudios de flexibilidad y

estabilidad en sistemas de puente de hidrógeno”. Universitat de Barcelona 2006.

Alberto Pérez. Doctoral Thesis. “Estudios de mecanismos de interacción macromolecular”. Universtat de

Barcelona 2008.

Axel Bidon-Chanal. Doctoral Thesis. “Estudio teórico del transporte de ligandos en proteínas y de la afinidad

ligando receptor”. Universitat de Barcelona 2008

Agnes Noy. . Doctoral Thesis. “La Flexibilidad en los ácidos nucleicos. Un estudio de dinámica Molecular”.


Jordi Muñoz. Doctoral Thesis. “Estudio teórico de interacciones moleculares. Aplicaciones al diseño de

fármacos”. Universitat de Barcelona 2008.

Josep Ramon Goñi. Doctoral Thesis. “Les propietats físiques de l’ADN en escala genòmica”. Universitat de

Barcelona 2008.

Tim Meyer. Doctoral Thesis. “Protein Structure and Dynamics studied by Molecular Dynamics Simulations”.


Ignacio Soteras. Doctoral Thesis. “Estudios de modelización molecular en solución”. Universitat de

Barcelona 2009.


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SUMMARY OF THE SCIENTIFIC RECORD SCIENTIFIC PUBLICATIONS: 331

SCIENTIFIC PUBLICATIONS SINCE 2003: 80

PAPERS WITH ISI IF (rounded to nearest integer number) ≥ 7 62

PAPERS WITH ISI IF (2007-2011) ≥ 7 22

PAPERS WITH ISI IF (2007-2011) ≥ 9 14

CITATIONS: (excluding papers more than 10 authors) 9027

PAPERS WITH MORE THAN 100 CITATIONS 16

H-index (Google Scholar excluding papers with more than 10 authors) 53

Highest H-index for a Spanish Chemist in “ISI-Multidisciplinary Chemistry Area”. Number 5th in

“ISI-Chemistry Physics area”, Number 5th in “ISI-Biochemistry and Molecular Biology area”.

Tahen from http://indice-h.webcindario.com/

Publications in high profile journals since 1988 Nature 1 Nature Genetics 1 Chem.Rev. 1 Chem.Soc.Rev. 1 Acc.Chem.Res. 2 Curr.Op.Struct.Biol 1 Angew. Chem. 2 PNAS 3 J.Am.Chem.Soc. 33 Briefings Bioinf 1 Nucleic Acids Res. 15 Genome Biol 1 Structure 5 PLOS CB 2 Chem.Comm. 2 Bioinformatics 5 J.Biol.Chem. 2 J.Physiol 1 J.Med.Chem. 10 Biophys.J. 5 Chem.Eur.J. 3 J.Mol.Biol 7 J.Chem.Theor.Comp 12 J.Phys.Chem.B 17 PCCP 6

Publications in high profile journals since 2007 Nature 1 Nature Genetics 1 Acc.Chem.Res. 2 Curr.Op.Struct.Biol 1 Angew. Chem. 2 PNAS 2 J.Am.Chem.Soc. 5 Nucleic Acids Res. 5 Genome Biol 1 Structure 5 PLOS CB 2 Chem.Comm. 2 Bioinformatics 3 J.Biol.Chem. 1 J.Med.Chem. 2 Biophys.J. 3 Chem.Eur.J. 1 J.Mol.Biol 3 J.Chem.Theor.Comp 10 J.Phys.Chem.B 4 PCCP 3 Briefings Bioinf 1


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RESEARCH PAPERS (in bold representative papers, in italics papers with more than 100 citations in WOK)

1) M.Orozco and F.J.Luque. “POEMS, A Porgram for Outliers Elimination In Multidimensional Spaces”.

Comp.Appl. Bios., (NOW BIOINFORMATICS) 4, 381-385 (1988).

2) M.Orozco and R.Franco. “TEFOOL, A Program for Theoretical Drug Design in Microcomputers”.

Comp.Appl. Bios., (NOW BIOINFORMATICS) 5, 219-226 (1989).

3) M.Orozco and F.J.Luque. “POEAMS, A Program for Outliers Elimination In Anomalous

Multidimensional Spaces”. Comp.Appl. Bios., (NOW BIOINFORMATICS) 5, 241-242 (1989)

4) M.Orozco and F.Sanz. “A Study of Sampling Subspaces in the Design of Series of Bioactive Compounds

. An.Quim. 85, 27-33 (1989).

5) M.Orozco and F.Sanz. “Enhacement of Austel Method in Series Design”An.Quim. 85, 34-38 (1989).

6) M.Orozco, C.Lluis, J.Mallol, E.I.Canela and R.Franco. “Theoretical Approximation to the Reaction

Mechanism of Adenosine Deaminase”. Quant.Struct.Act.Relat., 8, 109-114 (1989).

7) M.Orozco, C.Lluis, J.Mallol, E.I.Canela and R.Franco. In Quantitative Structure-Activity Relationships in

Drug Design. J.Fauchere (ed). Alan R.Liss. NY 1989, pp 109-11

8) M.Orozco, E.I.Canela and R.Franco. “Theoretical Stuy of the Tautomerism of Adenosine and Formycin:

Fuctional Implications”. Mol.Phamacol., 35, 257-266 (1989).

9) M.Orozco and F.J.Luque. “On The Use of Mixed Basis Sets to Compute Accurate Molecular

Electrostatic Potentials”. Chem.Phys.Lett., 160, 305-310 (1989).

10) F.J.Luque and M.Orozco. “Reliability of the AM1 wavefunction to compute Molecular Electrostatic

Potentials”. Chem.Phys.Lett., 168, 269-275 (1990).

11) M.Orozco, E.I.Canela and R.Franco. “Theoretical Study of the Hydroxyl Nucleophilic Attack on the 6-

Aminopyrimidine Molecule: Functional Implications in the Reaction Mechanism of Nucleoside

Deaminative Enzymes”. J.Org.Chem., 55, 2630-2637 (1990).


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12) M.Orozco, E.I.Canela and R.Franco. “A Quantum Mechanical Study of the Enzymatic Deamination of

Benzoadenine Derivatives: A Theoretical Model of the Interactions Occurring between Nucleosides and

the Active Site of Adenosine Deaminase”. Eur.J.Biochem., 188, 155-163 (1990).

13) F.J.Luque, F.Illas and M.Orozco “Comparative Study of the Molecular Electrostatic Potential Obtained

from Different Wavefunctions. Reliability of the Semiempirical MNDO Wavefunction”. J.Comp.Chem.,

11, 416-430 (1990).

14) M.Orozco and F.J.Luque. “On the Use of AM1 and MNDO Wavefunctions to Compute Accurate

Molecular Electrostatic Charges”. J.Comp.Chem., 11, 909-923 (1990). 129 Citations

15) M.Orozco, E.I.Canela and R.Franco. “Diseny de Farmacs per ordinador” (review). Innovaciò

Tecnológica., 2, 13-15 (1990).

16) M.Orozco, C.Laughton, P.Herzyck and S.Neidle. “Molecular Mechanics Modelling of drug-DNA

Structures; the Effect of Differing Dielectric Treatment on Helix Parameters and Comparsion with a

Fully Solvated Model”. J.Biomol.Struct.Dyn., 8, 359-373 (1990).

17) M.Orozco and F.J.Luque. “A practical Procedure for the Determination of Electrostatic Charges of Large

Molecules”. J.Comp.Aided-Mol.Des., 4, 411-426 (1990).

18) M.Orozco and R.Franco. “Computer Simulated Process of Lead Optimization. A Student-Interactive

Program”. J.Chem.Ed., 67, 232-234 (1990).

19) M.Orozco, E.I.Canela, J.Mallol, C.Lluis and R.Franco. “Ab Initio Study of the Protonation and the

Tautomerism of the 7-Aminopyrazolopyrimidine Molecule”. J.Org.Chem.., 55, 753-756 (1990).

20) M.Orozco, R.Franco, J.Mallol and E.I.Canela. “Theoretical Study of the Acidic Strength of aminoacidic

Side Chains”. Bioorg.Chem., 18, 361-372 (1990).

21) M.Orozco, C.Lluis, J.Mallol, E.I.Canela and R.Franco. “Quantum Cehmical Study of the Electronic and

Conformational Charactersitics of Adenosine and 8-Substituted Derivatives; Functional Impliations in the

Mechanism of Reaction of Adenosine Deaminase”. J.Phar.Sci., 79, 133-137 (1990).

22) M.Orozco and F.J.Luque. “Diseño de Fármacos Asistido por Odernador” (review). NPQ., 14, 304-309

(1990).


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23) C.Aleman, E.I.Canela, R.Franco and M.Orozco. “A New Strategy for the Evaluation of Force Parameters

from Quantum Mechanical Computations”. J.Comp.Chem., 12, 664-674 (1991).

24) M.Orozco, D.Velasco, E.I.Canela and R.Franco. “Determination of the Conformational

Preferences of Adenosine at the Active Site of Deaminase”. J.Am.Chem.Soc., 112, 8221-8229 (1990).

25) F.J.Luque, M.Orozco, F.Illas and J.Rubio. “Effect of Electron Correlation on the Electrostatic

Potential Distribution of Molecules”. J.Am.Chem.Soc., 113, 5203-5210 (1991).

26) M.Orozco, E.I.Canela and R.Franco. “Theoretical Modelling of the Pharmacophore Charactersistics of

the Active Site of Adenosine Deaminase”. Pharmcochem. Library, 16, 327-330 (1991).

27) M.Orozco and F.J.Luque. “A Practical Approach to the Computation of the Electrostatic Energy in large

Molecules”. J.Mol.Struct. (THEOCHEM)., 254, 31-42 (1992).

28) M.Rubiralta, F.J.Luque, M.Orozco, A.Diez and I.Lopez. “Conformational Analysis of 2-Aryl-4-

Piperidones. Effect of the Indole Protecive Phenylsulfonyl Group”. Heterocycles., 34, 449-456 (1992).

29) M.J.Negre, M.Orozco and F.J.Luque. “A New Strategy for the Representation of Environment Effects in

Semiempirical Calculations Based on Dewar’s Hamiltonians”. Chem.Phys.Lett., 196, 27-36 (1992).

30) A.Parraga, M.Orozco and J.Portugal. “Experimental and Modelling Studies on DNA cleavage by

Elsamicin A” Eur.J.Biochem., 208, 227-233. 1992.

31) C.Alemán and M.Orozco. “On The Suitability of Semiempirical Calculations As Sources of Force-Field

Parameters”. J.Comp.Aided-Mol.Des., 6, 331-348. 1992.

32) M.Orozco and F.J.Luque. “Diseño Asistido por Ordenador de Nuevos Compuestos Químicos” (review).

Quimica e Industria. 38, 513-525. 1992

33) .- J.Gao, F.J.Luque and M.Orozco. “Induced dipole moments and atomic charges based in average

electrostatic potentials in solution”. J.Chem.Phys. 98, 2975-2982. 1993

34) - M.Orozco and F.J.Luque. “Molecular Interaction Potential (MIP). A new tool for the study of chemical

reactivity”. J.Comp.Chem. 14, 587-603. 1993.

35) M.Orozco and F.J.Luque. “Mono and multiconfigurationall ab initio study of bond stretching.

Implications in theoretical Force-Field parametrization”. J.Comp.Chem. 14, 881-894. 1993.


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36) F.J.Luque and M.Orozco. “Ab Initio study of the reactivity of planar and twisted amides. New insights

into the amide resonance”. J.Chem.Soc. Perkin Trans II. 2. 683-690. 1993.

37) M.Orozco, C.Alemán and F.J.Luque. “Force-Field parametrization from Quantum Mechanical data”.

Models in Chemistry. 130, 695-717. 1993.

38) F.J.Luque, M.J.Negre and M.Orozco. “An AM1-SCRF approach to the study of changes in molecular

properties induced by the solvent”. J.Phys.Chem. 19, 4386-4391. 1993.

39) C.Alemán, F.J.Luque and M.Orozco. “On the suitability of PM3-derived Molecular Electrostatic

Potentials”. J.Comp.Chem. 14, 799-808. 1993.

40) M.Orozco and F.J.Luque. “SCRF computation of the reactive characteristics of the DNA bases in water”.

Biopolymers. 33, 1851-1869. 1993.

41) M.Orozco and F.J.Luque. “Diseño Asistido por Ordenador de Nuevos Compuestos Químicos” (review).

AQEIC Boletín Técnico. 3, 113-129. 1993.

42) C.Alemán, F.J.Luque and M.Orozco. “A new scaling procedure to correct semiempirical MEP and MEP-

derived properties”. J.Comp.Aided-Mol.Design. 7, 721-742. 1993.

43) M.Orozco, W.L.Jorgensen and F.J.Luque. “A comparison between 6-31G*-based MST/SCRF and FEP

evaluations of the hydration free energy of small neutral molecules”. J.Comp.Chem. 14, 1498-1503

(1993).

44) F.J.Luque and M.Orozco. “Theoretical study of the cis<->trans isomerization of the peptidic bond in

vacuum and in aqueous environments”. J.Org.Chem., 58, 6397-6405 (1993).

45) F.J.Luque, M.Orozco, P.K.Bhadane and S.R.Gadre. “SCRF calculations of the effect of the water on the

topology of the molecular electrostatic potential”. J.Phys.Chem. 97, 9380-9384. (1993).

46) H.A.Carlson, T.B.Nguyen, M.Orozco and W.L.Jorgensen. “Accuracy of Free Energies of Hydration for

Organic Molecules from 6-31G* Derived Partial Charges”. J.Comp.Chem. 14, 1240-1244 (1993). 148

Citations.

47) M.Orozco, J.Tirado-Rives and W.L.Jorgensen. “Mechanism for the rotamase activity of FK506 binding

protein from MD simulations”. Biochemistry (USA), 32, 12864-12874 (1993).


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48) F.J.Luque, C.Alhambra and M.Orozco. “A comparison of NDDO and quasi-ab initio approaches to

compute semiempirical molecular electrostatic potentials”. J.Comp.Chem. 15, 12-22 (1994).

49) M.Orozco, F.J.Luque and A.Martinez. “El Diseño de fármacos y la supercomputación” (review). Tecni

Farma. 1 16-24. 1994.

50) M.Bachs, M.Orozco and F.J.Luque. “Optimization of solute cavities and van der Waals parameters in ab

initio MST-SCRF calculations of neutral molecules”. J.Comp.Chem. 15, 446-454 (1994). 133 Citations.

51) C.Alemán and M.Orozco. “PAPQMD/AM1 parametrization of the bonded term of aromatic molecules”.

Biopolymers, 34, 941-955 (1994).

52) M.Orozco and F.J.Luque. “Optimization of the cavity size for ab initio MST-SCRF calculations of

monovalent ions”. Chemical Physics. 182, 237-248 (1994).

53) F.J.Luque, M.Orozco, P.K.Bhadane and S.R.Gadre. “Effect of solvation on the shapes, sizes and

anisotropies of polyatomic anions via Molecular Electrostatic Potential topology: an ab initio Self

Consistent Reaction Field approach”. J.Chem.Phys. 100, 6718-6726 (1994).

54) F.J.Luque, M.Bachs and M.Orozco. “An optimized AM1/MST method for the SCRF representation of

solvated systems”. J.Comp.Chem. 15, 847-857 (1994).

55) J.Gallego, F.J.Luque, M.Orozco, C.Burgos, J.Alvarez-Builla, M.Rodrigo and F.Gago. “DNA sequence-

specificity reading by echinomycin: role of hydrogen bonding and stacking interactions”. Journal of

Medicinal Chemistry., 37, 1602-1609 (1994).

56) J.Gallego, F.J.Luque, M.Orozco and F.Gago. “Binding of Echinomycin to d(GCGC)2 and d(CCGG)2 :

Role of stacking interactions in the sequence-dependent formation of Hoogsteen base pairs”. Journal of

Biomolecular Structure and Dynamics, 12, 111-129 (1994).

57) F.J.Luque, J.Bravo, I.Fita and M.Orozco. “Bioingeniería por Ordenador”. Investigación y Ciencia.

Spanish Edition of Scientific American (review). 11, 34-36 (1994).

58) C.Alemán, F.J.Luque and M.Orozco. “Force Field parametrization of large biomolecules from quantum

mechanical data.”. In “Trends in QSAR and Molecular Modelling. Concepts, Computational Tools and

Applications. Prous Science. 1995, pp 215-218


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59) C.Alhambra, F.J.Luque and M.Orozco. “Determination of the hydration characteristics of bioorganic

molecules from a mixed quantum mechanical-molecular mechanics strategy. The molecular solvation

potential (MSP).”. In “Trends in QSAR and Molecular Modelling. Concepts, Computational Tools and

Applications. Prous Science. 1995, pp 238-240

60) C.Alemán, M.Orozco and F.J.Luque. “Multicentric charges for the accurate representation of electrostatic

interactions in force-field calculation of small molecules.” Chemical Physics”. 189, 573-584 (1994).

61) W.L.Jorgensen, M.Orozco, E.M.Duffy, D.L.Severance y J. Tirado-Rives. “Solvent effect on amide

isomerization and the mechanism of reaction of FKBP-12”. Abstracts of Papers of the American

Chemical Society, 27, 133 (1994).

62) M.Orozco, M.Bachs and F.J.Luque. “Development of optimized MST/SCRF methods for semiempirical

calculations. The MNDO and PM3 Hamiltonians”. J.Comp.Chem., 16, 563-575 (1995)

63) C.Alhambra, F.J.Luque and M.Orozco. “Molecular Solvation Potential (MSP). A new tool for the

Quantum Mechanical description of hydration in organic and bioorganic molecules”. J.Phys.Chem., 99,

3084-3092 (1995).

64) M.Orozco and F.J.Luque. “Theoretical study of the protonation and tautomerism of 7-

aminopyrazolopyrimidine in the gas phase and aqueous solution”. J.Am.Chem.Soc., 117, 1378-1386

(1995)

65) F.J.Luque, P.K.Bhadane, S.R.Gadre and M.Orozco. “Effect of solvation on the the charge distribution of

cations: an ab initio Self Consistent Reaction Field approach. Chem.Phys.Lett., 232, 509-517 (1995)

66) F.J.Luque, C.Alhambra, J.Estelrich and M.Orozco. “The tautomerism of neutral and protonated 6-thio-

guanine in the gas phase and aqueous solution. An ab initio study”.J. Org. Chem., 60, 969-976 (1995).

67) M.Orozco, F.J.Luque, D.Habibollah-Zadeh and J.Gao. “Polarization contribution to the free energy of

hydration”. J. Chem. Phys., 102, 6145-6152 (1995).

68) F.J.Luque, C.Alhambra and M.Orozco. “Contribution of solvent-polarization effects to bi-molecular

interactions”. J. Phys. Chem., 99, 11344-11349 (1995).

69) M.Orozco, C.Alhambra and F.J.Luque. “Metodologías teóricas para el estudio de la interacción droga-

receptor. Aplicaciones al diseño de nuevos fármacos. Parte I. Técnicas Macroscópicas, Microscópicas y

Cuánticas” (review). Industria Farmaceútica, 2, 59-64 (1995).


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70) M.Orozco, C.Alhambra and F.J.Luque. “Metodologías teóricas para el estudio de la interacción droga-

receptor. Aplicaciones al diseño de nuevos fármacos. Parte II. Técnicas Clásicas y Mixtas”. (review).

Industria Farmaceútica , 3, 43-48 (1995).

71) C.Laughton, F.J.Luque and M.Orozco. “Counterion distribution around DNA studied by Molecular

Dynamics and Quantum Mechanical simulations. Implications in the charge parametrization of the

phosphate group”. J. Phys.Chem 99, 11591-11599 (1995).

72) C.Alhambra, F.J.Luque, J.Portugal and M.Orozco. “Molecular Dynamics study of the mechanism of

binding of Elsamicin A to the DNA”. Eur.J. Biochem. 230, 555-566 (1995).

73) J.Bastida, C.Codina, P.Peeters, M.Rubiralta, M.Orozco, F.J.Luque and S.C.Chhabra. “Alkaloids from

Crinum kirkii”. Phytochemistry, 40, 1291-1293 (1995).

74) F.J.Luque, M.Bachs, C.Alemán y M.Orozco. “Simulación molecular y reactividad química: modelización

del solvente”. In La Recerca en la Facultat de Farmàcia. Monográfico conmemorativo del 150

aniversario de la Facultad de Farmacia. (M.Viñas, ed). PUU. Barcelona 1996, pp 163-175.

75) D.Miguel, A.Diez, Y.Blache, F.J.Luque, M.Orozco, R.Remuson, Y.Gelas-Mialhe and M.Rubiralta.

“Synthetic studies on Indole Alkaloids VIII. Synthesis and reactivity of asymmetric 2-Indolyl-4-

methylenepiperidines”. Tetrahedron., 51, 7527-7546 (1995).

76) F.J.Luque, J.M.Bofill and M.Orozco. “New strategies to incorporate the solvent polarization in SCRF and

FEP calculations”. J. Chem. Phys., 103, 10183-10191 (1995).

77) F.J.Luque, C.Alemán, M.Bachs, and M.Orozco. “Extension of the MST/SCRF method to organic

solvents. Ab Initio and semiempirical parametrization for neutral solutes in CCl4”. J.Comp.Chem., 17,

806-820 (1996).

78) J.Mestres, M.Solà, R.Carbó, F.J.Luque and M.Orozco. “Efect of solvation of the charge distribution of a

series of anionic, neutral and cationic species. A Quantum Molecular Similarity Study”. J.Phys.Chem.,

100, 606-610 (1996).

79) M.Orozco, C.Alhambra, X.Barril, J.M.López, M.A.Busquets and F.J.Luque. “Theoretical methods for the

representation of solvent”. J. Mol. Modelling, 2, 1-15 (1996).


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80) F.J.Luque, Y.Zhang, C.Alemán, M.Bachs, J.Gao and M.Orozco. “Solvent ettects in chloroform solution:

parametrization of the MST-SCRF continuum model”. J.Phys.Chem., 100, 4269-4276 (1996). 102

Citations.

81) M.Orozco, J.M.López, C.Colomines, C.Alhambra, M.A.Busquets and F.J.Luque. “Theoretical

representation of solvation in biochemical systems. From discrete solute-solvent interactions to bulk

solvation”. Int. J. Quant. Chem (special issue, CECAM) 60, 1179-1187 (1996).

82) M.Orozco and F.J.Luque. “Generalization of the Molecular Electrostatic Potential for the study of non-

covalent interactions”. In “Molecular Electrostatic Potentials. Concepts and Applications”. Theoretical

and Computational Chemistry Series. Vol 3. J.S.Murray and K.Sen (eds). Elsevier. Amsterdam. 1996.pp

181-218.

83) M.Orozco, R.Roca, C.Alemán, M.A.Busquets, J.M.Lopez and F.J.Luque. “Theoretical methods for the

representation of solvent in biochemical systems”. Journal of Molecular Structure (THEOCHEM, special

issue),371, 269-278 (1996).

84) M.Orozco, C.Colomines and F.J.Luque. “Theoretical determination of the solvation free energy in water

and chloroform of the nuclei acid bases”. Chemical Physics 209, 19-29 (1996).

85) C.Colominas, F.J.Luque and M.Orozco. “Tautomerism and protonation of guanine and cytosine.

Implications in the formation of triplex DNA”. J. Am. Chem. Soc., 118, 6811-6821 (1996). 192

Citations.

86) B.Hernández, F.J.Luque and M.Orozco. “Tautomerism of Xanthine Oxidase Subtrates Hypoxathine and

Allopurinol”. Journal of Organic Chemistry, 61, 5964-5971 (1996).

87) B.Hernández, M.Orozco and F.J.Luque. “Tautomerism of xanthine and alloxanthine. A model for the

substrate-recognition by Xanthine Oxidase”. Journal of Computer-Aided Molecular Design , 10, 535-544

(1996).

88) F.J.Luque, B.Hernández, J.Lizondo, X.Barril and M.Orozco. “Química Computacional, ¿Hacia una

nueva alquimia? (review). AQEIC., 4, 182-194 (1996).

89) C.Alemán, R.Roca, F.J.Luque and M.Orozco. “Helical preferences of alanine, glycine and

aminoisobutyric peptides”.Proteins., 28, 89-93 (1997).


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90) R.Soliva, M.Orozco and F.J.Luque. “On the suitability of density functional methods for calculation of

electrostatic properties”. Journal of Computational Chemistry, 18, 980-991 (1997).

91) P.Camps, F.J.Luque, M.Orozco, F.Pérez and S.Vázquez. ”Synthesis, chemical trapping and dimerization

of tricyclo[3.3.0.03,7]oct-1(5)-ene, the consumate member of a series of pyramidalyzed alkenes”.

Tetrahedron Letters (1996) 37, 8605-8608

92) B.Hernández, M.Orozco and F.J.Luque. “Role of tautomerism of 2-azaadenine and 2-azahypoxanthine in

substrate recognition by xanthine oxydase”.Journal of Computer-Aided Molecular Design (1997) 11,

153-162.

93) M.Orozco and F.J.Luque. “Generalized linear free energy response theory”. Chemical Physics Letters

265, 473-480 (1997).

94) M.Orozco, C.Vega, A.Parraga, I.García-Saez, M.Coll., S.Walsh, T.J.Mantle and F.J.Luque.”On the

reaction mechanism of class π Clutathione S-transferase”. Proteins , 28, 530-542 (1997).

95) C.Alhambra, F.J.Luque, F.Gago and M.Orozco. “Ab initio investigation of stacking interactions in A-

and B-DNA”. Journal of Physical Chemistry B, 101, 3846-3853 (1997).

96) J.Tirado-Rives, M.Orozco and W.L.Jorgensen. “Molecular dynamics simulation of the unfolding of

barnase in water and 8M urea”. Biochemistry, 36, 7313-7329 (1997). 117 Citations

97) G.Shields, C.Laughton and M.Orozco. “Molecular dynamics simulations of the d(T.A.T) triple helix”.

J.Am.Chem.Soc , 119, 7463-7469 (1997). 107 Citations.

98) F.J.Luque and M.Orozco. “A new semiclassical-continuum representation of solvation”.Journal of

Physical Chemistry B, 101, 5573-5582 (1997).

99) F.J.Luque, J.M.Bofill and M.Orozco. “Reply to the Comments on the first order perturbation treatment of

solvation” Journal of Chemical Physics , 107, 1293-1294 (1997).

100) F.J.Luque, J.M.López-Bes, J.Cemelí, M.Aroztegui and M.Orozco. “Solvent effects on the

tautomerism equilibria of heterocycles”. Theoretical Chemistry Accounts (Theoretica Chimica Acta) 96,

105-113


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101) R. Soliva, F.J.Luque and M.Orozco. “Reliability of MEP and MEP-derived properties computed

from DFT methods for molecules containing P, S, and Cl”. Theoretical Chemistry Accounts (Theoretica

Chimica Acta) 98, 42-49 (1997).

102) M.Orozco and F.J.Luque. “Computer-assisted Drug Design. Current Status and Future Trends”.

Meth. Find Exp Clin Pharmacol 19, 33-35 (1997)

103) F.J.Luque and M.Orozco. “Metodologies computacionals per a l’estudi de macromolècules”.

Publicacions anuals de la Societat Catalana de Biologia. L.Cormudella ed. Vol 38, pp 73-92 (1998).

104) C.Colominas, J.Teixidó, J.Cemelí, F.J.Luque and M.Orozco. “Dimerization of carboxylic acids:

reliability of theoretical calculations and the effect of solvent”. J. Phys.Chem.B. 102, 2269-2276 (1998).

105) F.J.Luque and M.Orozco “Introduction of polarization in the Generalized Molecular Interaction

Potential. Definition of a new Hamiltonian for reactivity studies, and mixed QM/MM

calculations”.J.Comp.Chem 19, 866-881 (1998).

106) X. Barril, C.Alemán, M.Orozco and F.J.Luque. “Salt-bridge interactions: Stability of the ionic and

neutral complexes in the gas phase, in solution, and in proteins”. Proteins 32, 67-79 (1998).

107) E. Cubero, M.Orozco and F.J. Luque. “Azidomethine-Tetrazole isomerims in solution: A

themochemical study”. J. Org. Chem 63, 2354-2356 (1998).

108) G. Shields, C.Laughton and M.Orozco. “Molecular Dynamic simulations of the

PNA.DNA.PNA triple helix in aqueous solution”. J. Am. Chem. Soc., 120, 5895-5904 (1998).

109) E.Cubero, M.Orozco and F.J.Luque. “Theoretical study of azidoazomethine-tetrazole

isomerism: effect of solvent and substituents, and the mechanism of isomerization”. J. Am. Chem.

Soc., 120, 4723-4731 (1998).

110) C.Colominas, M.Orozco, F.J.Luque, J.I.Borrell, J.Teixidó.”A priori prediction of substituent and

solvent effects in nitrile basicity”. J. Org. Chem., 63, 4947-4953 (1998).

111) E.Cubero, F.J.Luque and M.Orozco. “Is polarization important in cation-ππππ interactions”. Proc.

Natl. Acad. Sci (USA)., 95, 5976-5980 (1998). 177 Citations.


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112) B.Luisi, M.Orozco, J.Sponer, F.J.Luque and Z.Shakked. “On the potential role of the amino nitrogen

atom as a hydrogen bond acceptor in macromolecules”. J. Mol. Biol. 279, 1123-1136 (1998).

113) M.Orozco, B.Hernández and F.J.Luque. “Tautomerism of 1-Me-uracil, 1-Me-thymine, and 1-Me-5-

Br-uracil. Is tautomerism the reason for the mutagenicity of 5-Br-uridine?”. J.Phys.Chem.B., 102, 5228-

5233 (1998).

114) R.Soliva, C.A.Laughton, F.J.Luque and M.Orozco. “Molecular dynamic simulations of

d(G.C.C) triple helix in aqueous solution”. J.Am.Chem.Soc. 120, 11226-11233 (1998).

115) F.J.Luque, J.M.López, M.López, C.Vicent, and M.Orozco. “Role of intramolecular hydrogen-bonds

in the intermolecular hydrogen-bonding of carbohydrates”. J.Phys.Chem.A., 102, 6690-6696 (1998).

116) F.J.Luque, X.Barril and M.Orozco. “A new method for the fractional description of solvation free

energies. Application in drug-design”. J.Comp-Aided Mol.Design, 13, 139-153 (1999).

117) E.Jiménez, A.Vaquero, M.L.Espinás, R.Soliva, M.Orozco, J.Bernués and F.Azorín. “The GAGA-

factor of Drosophila binds triple-stranded DNA”. J.Biol.Chem., 273, 24640-24648 (1998).

118) M.Orozco, C.Colominas, X.Barril and F.J.Luque. “Use of SCRF methods in drug design studies”. In

Molecular Modelling and Prediction of Bioactivity. K.Gundertofte and F.S.Jorgensen (ed). Kluwer

Academic/ Plenum Press., New York (2000), pp 129-134.

119) M.Orozco, E.Cubero, X.Barril, C.Colominas and F.J.Luque. “Nucleic Acid Bases in Solution”. In

Computational Molecular Biology. Theoretical Computational Chemistry. Vol 8. J.Leszczynski (ed).

Elsevier Science. Amsterdam. 1999, Chapter 4. Pages 119-166.

120) C.Colominas, J.Teixidó, F.J.Luque and M.Orozco. “Cavitation contribution to the free energy of

solvation. Comparison of different formalisms in the context of MST calculations”. Chemical Physics,

240, 253-264 (1999).

121) R.Güimil, A.Bachi, R.Eritja, F.J.Luque and M.Orozco. “Triple helix stabilization properties of

oligonucleotides containing 8-amino-2´-deoxyguanosine”. Bioorganic and Medicinal Chemistry Letters

8, 3011-3016 (1998).

122) E.Cubero, M.Orozco and F.J.Luque. “A topological analysis of electron density in cation-π

complexes”. J.Phys.Chem.A.,. 103, 315-320 (1999).


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123) C. Colominas, F.J.Luque and M.Orozco. “Monte Carlo-MST: A new strategy for the representation

of solvent configurational space in solution”. J. Comp. Chem ., 20, 665-678 (1999).

124) P.Camps, R.El Achab, D.Görbig, J.Morral, D.Muñoz-Torrero, A.Badia, J.E. Baños, N.M.Vivas,

X.Barril, M.Orozco and F.J.Luque. “Sythesis, in vitro pharmacology and molecular modeling of very

potent Tacrine-Huperzine A hybrids as Acetylcholinesterase inhibitors of potential interest for the

treatment of Alzheimer’s disease”. J. Med. Chem ., 42, 3227-3242.

125) E. Sherer, S.A.Harris, R. Soliva, M. Orozco and C.A. Laughton. “Molecular dynamics studies

of DNA A-tract structure and flexibility”. J. Am. Chem. Soc. 121, 5981-5991 (1999).

126) F.J.Luque, J.M.López and M.Orozco. “Perspective on ‘Electrostatic interactions of a solute with a

continuum. A direct utilization of ab initio molecular potentials for the prevision oc solvent effects’ by

S.Miertus, E.Scrocco and J.Tomasi”. Theoretical Chemistry Accounts Special New Century Issue 103,

343-345 (2000).

127) M. Forés, M. Durán, M. Solà, M.Orozco and F.J.Luque. “Theoretical evaluation of solvent effects on

the conformational and tautomeric equilibria of 2-(2’-hydrodyphenyl)benzimidazole and on its absortion

and fluorescence spectra”. J. Phys. Chem.A. 103, 4525-4532 (1999).

128) R.Güimil, E. Ferrer, N.J. Macias, R. Eritja and M. Orozco. “Theoretical calculations, synthesis

and base-pairing properties of oligonucleotides containing 8-amino-2´-deoxyadenosine”. Nucleic

Acid Research 27, 1991-1998 (1999).

129) E. Cubero, M.Orozco P. Hobza and F.J.Luque. “Hydrogen bond versus anti-hydrogen bond: A

comparative analysis based on the electron density topology”. J. Phys. Chem.A., 103, 6394-6401 (1999).

148 Citations.

130) M. De Rosa, R.P. Issac, M.Marquez, M.Orozco, F.J.Luque and M.D. Timken. “2-aminopyrrole and

simple 1-substitued 2-aminopyrroles: Preparation and ab initio study on the effect of solvent on the

amino-imino tautomeric equilibrium”. J.Chem.Soc. Perkin II., 1433-1437 (1999).

131) R.Soliva, F.J.Luque and M.Orozco. “Can G•C Hoogsteen-wobble pair contribute to the

stability of d(G•C•C) triplexes?”. Nucleic Acid Research. 27, 2248-2255 (1999).

132) C.Colominas, F.J.Luque and M.Orozco. “Dimerization of formamide in gas phase and solution. An

ab initio MC-MST study”. J. Phys.Chem.A., 103, 6200-6208 (1999).


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133) R.Soliva, F.J. Luque, C. Alhambra and M.Orozco. “Role of sugar re-puckering in the transition

between A and B forms of DNA in solution. A molecular dynamics study”. J.Biomol.Struct.Dyn., 17, 89-

99 (1999).

134) E. Cubero, E.C.Sherer, F.Javier Luque, M.Orozco and C.A.Laughton. “Observation of a

spontaneous base pair breathing event in the molecular dynamics simulation of a difluorotoluene-

containing DNA oligonucleotide”. J. Am.Chem.Soc., 121, 8653-8654 (1999).

135) B.Hernández, F.J.Luque and M.Orozco. “Parametrization of the GMIPp for the study of stacking

interactions”. J. Comp. Chem. 20, 937-946 (1999).

136) E.Cubero, M.Orozco and F.J.Luque. “Electron density topological analysis of the C-H...O Anti-

Hydrogen bond in fluroforom-ethylene oxide complex”. Chemical Physics Letters 310, 445-450 (1999).

137) M.Orozco, E.Cubero, B.Hernández, J.M.López and F.J.Luque. “Interactions of nucleic acid bases”:

The role of solvent. In Computational Chemistry. Reviews of Current Trends. Vol 4. J.Leszczynski (ed).

World Scientific Publishing. Singapore. 1999. Chapter 4, pp 191-225.

138) R.Eritja, E.Ferrer, R.Güimil and M.Orozco. “Modified Oligonucleotides with triple-helix

stabilization properties”. Nucleosides and Nucleotides. 18, 1619-1621 (1999).

139) X.Barril, M.Orozco and F.J.Luque. “Predicting relative binding free energies of Tacrine.Huperzine A

hybrids as inhibitors of Acetylcholinesterase”. J. Med. Chem., 42, 5110-5119 (1999).

140) B.Hernández, F.J.Luque and M.Orozco. “Mixed QM/MM Molecular Electrostatic Potentials”.

J.Comp. Aided Mol. Des., 14, 329-339 (2000).

141) J.Muñoz, X.Baril, F.J.Luque, J.L.Gelpí and M.Orozco. “Partitioning of free energies of solvation into

fragment contributions: Applications in drug design”. In Advances in Molecular Similarity. Vol 4.

R.Carbó-Dorca, X.Gironés and P.G.Mezey (eds). Kluwer Ed. Amsterdam 2001. Pp 143-168.

142) B.Hernández, R.Soliva, F.J.Luque and M.Orozco. “Misincorporation of 2’-deoxyoxanosine

into DNA: A molecular basis for NO-induced mutagenesis derived from theoretical calculations”.

Nucl. Acid. Res, 28, 4873-4883 (2000).

143) M. Amat, J. Bosch, J. Hidalgo, M. Cantó, M.Pérez, N. Llor, E. Molins, C.Miravitlles, M.Orozco and

F.J.Luque. “Synthesis of enantiopure trans-3,4-disubstituted piperidines. An enantiodivergent synthesis

of (+)- and (-)-paroxetine”. J.Org.Chem., 65, 3074-3084 (2000). 102 Citations.


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144) X.Barril, J.Muñoz, F.J.Luque and M.Orozco. “Simplified descriptions of the topological distribution

of hydrophilic/hydrophobic characteristics of molecules”. Physical Chemistry Chemical Physics, 2, 4897-

4905 (2000).

145) E.Cubero, C.A.Laughton, F.J.Luque and M.Orozco. “Molecular dynamics study of

oligonucleotides containing difluorotoluene”. J.Am.Chem.Soc., 122, 6891-99 (2000)

146) R.Soliva, E.Sherer, F.J.Luque, C.A.Laughton and M.Orozco. “Molecular dynamics simulations of

PNA•DNA and PNA•RNA duplexes in aqueous solution”. J.Am.Chem.Soc., 122, 5997-6008 (2000).

147) P.Hobza, J.Sponer, E.Cubero, M.Orozco and F.J.Luque. “C-H•••O contacts in the Adenine•Uracil

Watson-Crick and Uracil•Uracil nucleic acid base pairs. Nonempirical ab initio study with inclusion of

electron correlation effects”. J.Phys.Chem.B, 104, 6286-6292 (2000).

148) P.Camps, R.El Achab, D.Görbig, J.Morral, D.Muñoz-Torrero, A.Badia, J.E. Baños, N.M.Vivas,

X.Barril, M.Orozco and F.J.Luque. “New Tacrine-Huperzine A hybrids (Huprines): Highly potent tight-

binding Acetylcholinesterase inhibitors for the treatment of Alzheimer´s disease”. J. Med. Chem., 43,

4657-4666 (2000).

149) M.Orozco and F.J.Luque. “Theoretical methods for the representation of solvent in biomolecular

systems”. Chem.Rev. 100, 4187-4225 (2000). 353 citations

150) E.Guàrdia, R. Pinzón, J. Casulleras, M.Orozco and F.J. Luque. “A Computer simulation study of

liquid acetonitrile with an ab initio three site potential”. Mol. Simul., 26, 287-306 (2001).

151) X.Barril, J.L.Gelpí, J.M.López, M.Orozco and F.J.Luque. “How accurate can MD/LR and PB/SA

calculations be for predicting relative binding affinities?. Acethylcholinesterase Hiprine inhibitors as a

test case”. Theor. Chem. Acc., 106, 2-9 (2001).

152) C.Busquets, B.Merinero, E.Christensen, J.Gelpí, J.Campistol, M.Pineda, E.Fernández-Alvárez,

J.Prats, A.Sans, R.Arteaga, M.Martí, J.Campos, M.Martínez-Pardo, A.Martínez-Bermejo, M.L. Ruiz-

Falcó, J.Vaquerizo, M.Orozco, M.Ugarte, M.J.Coll and A.Ribes. “Glutaryl-CoA Dehydrogenase

Deficiency in Spain: Evidence of Two Groups of Patients, Genetically, and Biochemically Distinct”.

Pediatric Research, 48, 315-322 (2000).


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153) R.Soliva, R.Güimil-García, J.R.Blas, R.Eritja, J.L.Asensio, C.González, F.J.Luque and

M.Orozco. “DNA-triple strabilizing properties of 8- aminoguanine”. Nucleic Acid Research, 28,

4531-4539 (2000).

154) C.Curutchet, M.Orozco and F.J.Luque. “Solvation in octanol: Parametrization of the continuum MST

model”. J.Comput.Chem., 22, 1180-1193 (2001).

155) R.Soliva, V.Monaco, N.J.Meeuwenoord, G.A.Van der Marel, J.M.Van Boom, C.González and

M.Orozco. “Solution structure of a DNA duplex with a chiral alkyl-phosphonate moiety”. Nucleic

Acids Res. 29, 2973-2985 (2001).

156) A.Aviñó, J.C.Morales, M.Frieden, B.G.de la Torre, R.Güimil García, E.Cubero, F.J.Luque,

M.Orozco, F.Azorín and R.Eritja. “Parallel-stranded hairpins containing 8-aminopurines. Novel and

efficient probes for triple-helix formation.” Bioorganic Med. Chem. Lett. 11, 1761-1763 (2001).

157) E.Cubero, R.Güimil-García, F.J.Luque, R.Eritja, and M.Orozco. “The effect of amino groups

on the stability of DNA duplexes and triplexes ased on purines derived from inosine”. Nucleic

Acid.Res. 29, 2522-2534 (2001).

158) J.L.Gelpí, S.Kalko, X de la Cruz, X.Barril, J.Cirera, F.J.Luque and M.Orozco.. “Classical Molecular

Interaction Potentials: An improved set-up procedure in molecular dynamics simulations of proteins”.

Proteins 45, 428-437 (2001).

159) X.Barril, M.Orozco and F.J.Luque. “Towards improved Acettylcholinesterase inhibitors: An

overview of molecular modeling and computational approaches”. Minireviews in Medicinal Chemistry 1,

255-266 (2001).

160) M. Rueda, F.J. Luque, J.M. López and M. Orozco. “Amino-imino tautomerism in derivatives of

cytosine: effects on hydrogen bonding and stacking properties”. J.Phys.Chem A. 105, 6575-6580 (2001).

161) J.Muñoz, J.Sponer, P.Hobza, M.Orozco and F.J.Luque. “of hydrated Mg2+ cation with bases, base

pairs and nucleotides. Electron topology, Natural Orbital and vibrational study”. J.Phys.Chem.B., 105,

6051-6060 (2001).

162) M.Rueda, F.J.Luque and M.Orozco. “A theoretical investigation on the effect of remote amino

groups in hydrogen bonding of nucleic acids”. Biopolymers 61, 52-60 (2002).


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163) R.Lavilla, O.Coll, J.Bosch, M.Orozco and F.J.Luque. “General access to tacamine and vinca-eburna

alkaloids through tandem non-biomimetic oxidation of dihydropyridines/Zn mediated radical addition

processes. Unexpected facial selectivity of flattened cyclohexyl-type radicals”. Eur.J. Org. Chem, 2001,

3719-3729 (2001).

164) S.Kalko, J.L.Gelpí, I.Fita and M.Orozco. “Theoretical study of the mechanisms of substrate

recognition by Catalase”. J.Am.Chem.Soc. 123, 9665-9672 (2001).

165) J.Muñoz, X.Fradera, M.Orozco and F.J.Luque. “Topological analysis of hydrogen-bonded

complexes”. In Reviews in Moder Quantum Chemistry. A Celebration of the Contributions of R.G.Parr.

K.D.Sen (ed). World Scientific Press. Singapore. 2002 pp. 1615-1641.

166) S.A.Harris, E.Gavathiotis, M.S.Searle, M.Orozco and C.A.Laughton. “Co-operativity in drug-

DNA recognition: a molecular dynamics study”. J.Am.Chem.Soc. (2001) 123, 12658-12663. 108

Citations.

167) J. Muñoz, X.Barril, J.M.López, M.Orozco and F.J.Luque. “Solvation effects on the hydrogen-bonded

complexes of nucleic acid bases: A hydrophobic similarity study”. In “Advances in Molecular

Similarity”. R.Carbó, X.Gironés and P.G.Mezey (ed). Kluwer Academic Press. In Press. 2001.

168) E.Cubero, F.J.Luque and M.Orozco. “Theoretical studies of d(A:T)-based parallel-stranded

DNA duplexes”. J.Am.Chem.Soc. 123, 12018-12025 (2001).

169) P. Camps, E.Gómez, D.Muñoz-Torrero, A.Badia, N.María, X.Barril, M.Orozco and F..Luque.

“Synthesis in vitro pharmacology and molecular modeling of Syn-Huprines as acetylcholinesterase

inhibitors”. J. Med. Chem., 44, 4733-4736 (2001).

170) X.Fradera, X.de la Cruz, C.H.T.P.Silva, J.L.Gelpí, F.J.Luque and M.Orozco. “How depednent are

binding sites of the bound ligand”. Bioinformatics (2002). 18, 939-948 (2002).

171) C.Chipot, F.Dehez, J.Angyán, C.Millot, M.Orozco and F.J.Luque. “Alternative approaches for the

calculation of induction energies. Characterization, effectiveness and pitfalls”. J.Phys.Chem. A, 105,

11505-11514 (2001).

172) E.Cubero, A.Aviñó, B.G.de la Torre, M.Frieden, R.Eritja, F.J.Luque, C.González and

M.Orozco. “Hoogsteen-based parallel-stranded duplexes of DNA. The effect of 8-amino

derivatives”. J.Am.Chem.Soc (2002) 124, 3133-3142.


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173) H. Dvir, D.M. Wong, M. Harel, X. Barril, M. Orozco, F. J. Luque, D. Muñoz-Torrero, P. Camps, T.

A. Rosenberry, I. Silman, and J. L. Sussman. “3D Structure of acetylcholinesterase complexed with

Huprine X at 2.1 Å: Kinetic and Molecular Dynamics correlates”. Biochemistry (2002), 41, 2970-2981.

174) C.Ferrer, M.Orozco and X de la Cruz. “Characterization of disease-associated single aminoacid

polymorphisms: A first step towards understanding the molecular basis of disease”. J.Mol.Biol. (2002)

315, 771-786.

175) J.Muñoz, X.Barril, B.Hernández, M.Orozco and F.J. Luque. “Hydrophobic similarity between

molecules: A MST-based hydrophobic similarity index”. J.Comp.Chem. (2002). 23, 554-563.

176) X.Barril, S.Kalko, M.Orozco and F.J.Luque. “Rational design of reversible acetylcholinesterase

inhibitors”. Minireviews in Medicinal Chemistry (2002). 2, 27-36.

177) S.Kalko, J.L.Gelpí and M.Orozco. “The impact of H2O2 on the structure of catalases by molecular

modelling methods”. In “Biophysical Chemistry: Membranes and Proteins”. R.H.Templer and

R.Leatherbarrow (eds). Publications of the Royal Society of Chemistry. London 2002. pp 78-84.

178) J.Robles, A.Grandas, E.Pedroso, F.J.Luque, R.Eritja and M.Orozco. “Nucleic acid triple helices.

Stability effects of nucleobase modifications”. Current Organic Chemistry (2002) 6, 1333-1368.

179) B.Hernández, C.Curutchet, C.Colominas, M.Orozco and F.J.Luque. “Prediction of conformational

free energy differences of solutes in solution. An MC-MST study”. Mol. Simul. (2002) 28, 153-171.

180) A.Aviñó, M.Frieden, J.C.Morales, B.G. de la Torre, R.Güimil-Garcia, F.Azorín, J.L.Gelpí,

C.González, M.Orozco and R.Eritja. “Properties of triple-helix formed parallel-stranded hairpins

containing 8-aminopurines”. Nucleic Acids Research. (2002) 30, 2609-2619

181) C.Curutchet, C.J.Cramer, D.G.Truhlar, M.Ruiz-López, M.Orozco and F.J.Luque. “Electrostatic

interactions in Solvation: Comparison of SCRF continuum models”. J.Comp.Chem. (2003) 24, 284-297.

182) J.Ribas, E.Cubero, F.J.Luque and M.Orozco. “Theoretical study of the alkyl-π and aryl-π

interactions. Reconciling theory and experiments”. J.Org.Chem. (2002), 67, 7057-7065.

183) S.A.Trygubenko, T.V.Bogdan, J.Sponer, M.Rueda, M.Orozco, F.J.Luque, P.Slavíek and P.Hobza.

“Correlated ab initio study of nucleic adis bases and their tautomers in the gas phase and aqueous

solition.1. Cytosine”. Phys. Chem & Chem.Phys., (2002) 4, 4192-4203.


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184) C.Curutchet, A.Salichs, M.Orozco and F.J.Luque. “Transferability of fragmental contributions to the

octanol/water partition coefficient. An NDDO-based study”. J.Comp.Chem. (2002), 24, 32-45.

185) A.Salichs, N.López, V.Segarra, M.Orozco and F.J.Luque. “Fast estimation of hydrogen-bonding

donor and acceptor propensities. A GMIPp study”. Journal of Computer-Aided Molecular Design (2002),

16, 569-583.

186) J.Muñoz, J.L.Gelpí, M.Soler-López, J.A.Subirana, M.Orozco and F.J.Luque. “Can divalent cations

stabilize the triplex motif?. Theoretical study of the interaction of hydrated Mg2+ with the G*G-C triplet.”

J.Phys.Chem. B. (2002), 106, 8849-8857.

187) A.Castro, L.Hernández, I.Dorronsoro, P.Saenz, C.Pérez, S.Kalko, M.Orozco, F.J.Luque and

A.Martínez. “Synthesis, biological evaluation and modeling studies of dual binding AchE inhibitors.

Medicinal Chemistry Research (2002), 11, 219-237.

188) J.Ramón Blas, Manuel Márquez, Jonathan L. Sessler, F.Javier Luque and M.Orozco.

“Theoretical study of anion binding to calix[4]pyrr ole: The effect of solvent, fluorine substitution,

cosolute and water traces”. J.Am.Chem.Soc. (2002), 124, 12796-12805.

189) E.Cubero, F.J.Luque, M.Orozco and J.Gao. “A perturbational approach to combined QM/MM

simulation of Solute-Solvent Interactions in Solution”. J.Phys.Chem (2003) 107, 1664-1671.

190) C.Curutchet, J.M.Bofill, B.Hernández, M.Orozco and F.J.Luque. “Energy decomposition in

molecular complexes. Implication for the treatment of polarization in molecular simulations”.

J.Comp.Chem (2003) 10, 1263-1275.

191) N.Escaja, E.Pedroso, J.L.Gelpí, M.Orozco, M.Rico and C.González. “A four-stranded DNA

structure stabilized by a novel G:C:A:T tetrad”. J.Am.Chem.Soc. (2003) 125, 5654-5662.

192) R.Soliva, C.Almansa, S.G.Kalko, F.J.Luque and M.Orozco. “Theoretical studies on the inhibition

mechanism of COX-2. Is there an unique recognition site?”. J.Med.Chem. (2003) 46, 1372-1382.

193) X.Fradera, M de Rosa, M.Orozco and F.J.Luque. “Tautomeric conjugate acids of aminopyrroles:

Effect of substituents, solvation and co-solute”. Theor. Chem. Acc. (2004) 111, 223-230.

194) M.Rueda, S.Kalko, F.J.Luque and M.Orozco. “The structure and dynamics of DNA in the gas

phase”. J.Am.Chem.Soc. (2003) 125, 8007-8014.


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195) A.Morreale, J.L.Gelpí, F.J.Luque and M.Orozco. “Continuum and discrete calculation of fractional

contributions to solvation free energy”. J.Comp.Chem (2003) 24, 1610-1623.

196) X.Fradera, M.Márquez, B.Smith, M.Orozco and F.J.Luque. “Molecular Dynamics Study of

[2]rotaxanes: Influence of solvation and cation on co-conformation”. J.Org.Chem (2003) 68, 4663-4673

197) M.Orozco, A.Pérez, A.Noy and F.J.Luque. “Theoretical methods for the simulation of nucleic acids”.

Chem.Soc.Rev. (2003) 32, 350-364.

198) A.Aviño, M.Frieden, J.C.Morales, B.G. de la Torre, R.Güimil-García, M.Orozco, C.González and

R.Eritja. “Properties of triple helices formed by oligonucleotides containing 8-aminopurines”.

Nucleosides and Nucleotides. (2003), 22, 645-648.

199) A.Aviñó, E.Cubero, C.González, R.Eritja and M.Orozco. “Antiparallel triple helices.

Structural characteristics and stabilization by 8-amino derivatives”. J.Am.Chem.Soc. (2003), 125,

16127-16138.

200) F.J.Luque, C.Curutchet, J.Muñoz, A.Bidon-Chanal, A.Morreale, J.L.Gelpí and M.Orozco.

“Continuum solvation models: Dissecting the free energy of solvation”. Physical Chemistry and

Chemical Physics (2003) 5, 3827-3836.

201) E.Cubero, N.Abrescia, J.A.Subirana, F.J.Luque and M.Orozco. “Theoretical study of a new

structure of DNA: The antiparallel Hoogsteen duplex”. J.Am.Chem.Soc. (2003), 125, 14603-14612.

202) J. Muñoz-Muriedas, S.Perspicace, N.Bech, S.Guccione, M.Orozco and F.J.Luque. “Molecular

Alignment Based on Hydrophobic Similarity as a Tool in Drug Design”. J.Comput. Aided Mol. Design

(2005), 19, 401-419.

203) J.R.Blas, F.J.Luque and M.Orozco. “Unique tautomeric properties of isoguanine”.

J.Am.Chem.Soc. (2004), 126, 154-164.

204) M.Orozco, M.Rueda, J.R.Blas, E.Cubero, F.J.Luque and C.A.Laughton. “Molecular dynamics

simulation of nucleic acids”. Encyclopedia of Computational Chemistry (2003). In Press

205) R.Goñi, X de la Cruz and M.Orozco. “Triplex target sequences in the human genome”. Nuc.

Acid. Res (2004), 32, 354-360.


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206) A.Valenzuela, D. Talavera, M.Orozco and X. de la Cruz. “Alternative splicing and the modulation of

protein function among species”. J.Mol.Biol (2004), 335, 495-502.

207) R.Estévez, M.Pusch, C.Ferrer-Costa, M.Orozco and T.J.Jentsch. “Functional and Structural

Conservation of CBS domains for ClC Channels”. J.Gen.Physiol. (2004), 122,14.

208) I.Soteras, A.Morreale, J.M.López-Bes, M.Orozco and F.J.Luque. “Group contributions to the

solvation free energy from MST continuum calculations “. Braz. J. Phys. (2004), 34, 48-57.

209) C.Curuchet, A.Bidon-Chanal, M.Orozco and F.J.Luque. “MST study of group contributiuons for

alkane derivatives: Effect of the charge normalization”. Chem. Phys. Lett. (2004), 384, 299-305.

210) F.J. Luque, A.Bidon-Chanal, J.Muñoz-Muriedas, I.Soteras, C.Curutchet, A.Morreale and M.Orozco.

“Solute-solvent interactions from QM SCRF methods. Analysis of Group Contributions to Solvation”. In

Fundamental World of Quantum Chemistry. A tribute to the memory of Per-Olov Lowding. Volume 3.

Eds. E.Brandas, E.Kryachko. Kluwer 2004. pp 475-495.

211) R.Estévez, M.Pusch, C.Ferrer, M.Orozco and T.J.Jentsch.. “Functional and structural conservation of

CBS domains from CLC channels”. J.Physiology (2004), 557, 363-378.

212) J.L.Marco, C.de los Rios, A.G.Garcia, M.Villarroya, M.C.Carreiras, C.Martins, A.Eletéiro,

A.Morreale, M.Orozco and F.J.Luque “Synthesis, biological evaluation and molecular modelling of

diversely functionalized heterocyclic {Pyrano[3,2-e]pyridine,Pyrano[2,3b] quinoline,[1,8]

Naphthyridines,Oxazolo[4,5-e] pyridine and Oxazolo[5,4-b]quinoline} derivatives as

Acetylcholinesterase and Butyrylcholinesterase Inhibitors”. Bioorg. Med. Chem. (2004), 12, 2199-2218.

213) E.J. Stollar, J.L.Gelpí, S. Velankar, A. Golovin, M. Orozco and B. F. Luisi. “An unconventional

water-tryptophan interaction in protein structures”. Proteins (2004), 57, 1-8.

214) I.Gómez-Pinto, E.Cubero, S.G.Kalko, V.Monaco, G. Van der Marel, J.H. van Boom, M.Orozco and

C.González.. “Effect of bulky lesions on DNA: Solution structure of a DNA duplex containing a

cholesterol adduct.”. J.Biol.Chem., (2004), 279, 24552-24560.

215) C.Ferrer-Costa, M.Orozco and X. de la Cruz. “Prediction of pathological mutations with neural

networks using séquense information only”. Proteins (2004), 57, 811-819.

216) M.Rueda, E.Cubero, C.A.Laughton, M.Orozco. “Exploring the counterion atmosphere around DNA.

What can be learnt from molecular dynamics simulations?”. Biophys. J. (2004), 87, 800-811.


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217) L.Martí, A.Abella, X de la Cruz, S.García-Vicente M.Unzeta, C.Carpéné, M.Palacín, X.Testar,

M.Orozco and A.Zorzano. “Exploring the binding mode of semicarbazide-sensitive amine oxidase/VAP-

1: Identification of novel substrates with Insuline-like activity”. J.Med.Chem (2004), 47, 4865-4874.

218) J.Muñoz-Muriedas, J.M.López, M.Orozco and F.J.Luque. “Molecular Modeling Approaches to the

Design of Acetylcholinesterase Inhibitors: New Challenges for the Treatment of Alzheimer’s Disease”.

Current. Pharm. Des., (2004), 10, 3131-3140.

219) A.Noy, A.Pérez, P.Lankas, F.J.Luque and M.Orozco “The relative flexibility of DNA and RNA: A

molecular dynamics study”. J.Mol.Biol. (2004), 343, 627-638.

220) A.Morreale, X. De la Cruz, T.Meyer, J.L.Gelpí. F.J.Luque and M.Orozco. “Linear Response Theory:

An alternative to MM/PB and GB/SA methods for the analysis of molecular dynamics trajectories?

Proteins (2004), 57, 458-467.

221) A.Morreale, X de la Cruz, T,Meyer, J.L.Gelpí, F.J.Luque and M.Orozco. “Partition of protein

solvation into group contributions from molecular dynamics simulations.” Proteins (2004), 58, 101-109.

222) N.Spackova, E.Cubero, J.Sponer and M.Orozco. “Theoretical study of the guanine��6-

thioguanine substitution in duplexes, triplexes and tetraplexes.” J.Am.Chem.Soc (2004), 126, 14642-

14650.

223) A.Pérez, A.Noy, F.Lankas, F.J.Luque and M.Orozco “ The relative flexibility of DNA and

RNA: Database analysis. Nucleic Acids Res, (2004), 32, 6144-6151.

224) A.Crespo, M.A.Martí, S.G.Kalko, A.Morreale, M.Orozco, J.L.Gelpi, F.J.Luque and D.A.Estrin

“Theoretical study of the truncated hemoglobin HbN: Exploring the molecular basis of the NO

detoxification mechanism”. J.Am.Chem.Soc., (2005), 127, 4433-4444.

225) C.Ferrer-Costa, M.Orozco and X. de la Cruz. “How can non-human proteins accommodate as wild-

type human disease-associated residues”. Proteins(2005), 61, 878-887.

226) A.Noy, A.Pérez, M.Márquez, F.J.Luque and M.Orozco. “Structure, recognition properties and

flexibility of the DNA·RNA hybrid”. ”. J.Am.Chem.Soc., (2005), 127, 4901-4920.

227) C.Curutchet, A.Bidon-Chanal, I.Soteras, M.Orozco and F.J.Luque. “MST continuum study of the

hydration free energies of monovalent ionic species”. J.Phys.Chem.B (2005) 109, 3565-3574.


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228) L.Conde, J.M.Vaquerizas, C.Ferrer-Costa, Xavier de la Cruz, M.Orozco and J.Dopazo.

“PupasView: A visual tool for selecting suitable SNPs with putative pathological effects in genes for

geotyping purporses”. Nucleic Acid. Res., (2005), 33, W501-505.

229) A.Pérez, J.Sponer, P.Jurecka, P.Hobza, F.J.Luque and M.Orozco. “Are the RNA(A·U) hydrogen

bonds stronger than the DNA(A·T) ones?.” Chemistry an European Journal(2005) 11, 5062-5066

230) C.Ferrer-Costa, J.L.Gelpí, L.Zamakola, I.Parrága, X de la Cruz and M.Orozco. “PMUT: A Web-

based tool for the annotation of pathological mutations on proteins”. Bioinformatics (2005), 21, 3176-

3178. 128 Citations

231) M. Rueda, F.J Luque and M .Orozco. “The nature of minor-groove binders-DNA complexes in

the gas phase”. J.Am.Chem.Soc., (2005), 127, 11690-98.

232) O.Huertas, J.R.Blas I.Soteras, M.Orozco and F.J.Luque. “Benzoderivatives of nucleic acid bases as

modified DNA building blocks”. J.Phys.Chem.A., ., (2006), 110, 510-518.

233) D.Alonso, I.Dorronsoro, L.Rubio, P.Muñoz, E.García-Palomero, M.Del Monte, A.Bidon-Chanal,

M.Orozco, F.J.Luque, A.Castro, M.Medina and A.Martínez. “ Donepezil-Tacrine hybrid related

derivatives as new dual binding site inhibitors of AchE” Bioorg. Med. Chem. ., (2005), 13, 6588-97.

234) Alberto Pérez, José Ramón Blas, Manuel Rueda, Jose María López-Bes, Xavier de la Cruz, and

Modesto Orozco. “Exploring the essential dynamics of B-DNA” Journal of Chemical Theory and

Computation., (2005), 1, 790-800.

235) P.Muñoz-Ruiz, L.Rubio, E.Garcia-Palomero, M del Monte-Millán, P.Usán, I.Dorronsoro,

M.Bartolini, A.Bidon-Chanal, M.Orozco, F.J.Luque, M.Medina and A.Martínez. “Design, Synthesis and

Pharmacological Evaluation of Dual Binding Site Acetylcholinesterase Inhibitors: New Disease

Modifying Agents for Alzheimer’s Disease”. J.Med.Chem (2005) 48,7223-7233.

236) E.Cubero, F.J.Luque and M.Orozco. . “Theoretical study of the Hoogsteen��Watson-Crick

junctions in DNA”. Biophys. J. (2006), 90, 1000-1008.

237) I.Soteras, C.Curutchet, A.Bidon-Chanal, M.Orozco and F.J.Luque “Extension of the MST model to

the IEF formalism: HF and B3LYP parametrizations” J.Mol.Struct. (THEOCHEM), (2005), 727, 29-40.


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238) J. López de la Osa, C.González, R.Gargallo, E.Cubero, A.Aviñó, M.Orozco and R.Eritja.

“Destabilization of quadruplex DNA by 8-aminoguanine”. ChemBiochem. (2006), 7, 46-48.

239) Agnes Noy, Tim Meyer, Manuel Rueda, Carles Ferrer, Antonio Valencia, Alberto Pérez, Xavier de

la Cruz, J.M.López-Bes, F. Javier Luque and Modesto Orozco. “Datamining of molecular dynamics

trajectories of nucleic acids”. J.Biomol.Struct.Dynam (2006), 23, 447-456.

240) M.Rueda, F.J.Luque and M.Orozco “G-DNA can maintain its structure in the gas phase”.

J.Am.Chem.Soc. (2006), 128, 3608-3619.

241) J.Sponer, P.Jurecka, I.Marchan, F.J.Luque, M.Orozco and P.Hobza. “Nature of base stacking.

Reference quantum chemical stacking energies in ten unique B-DNA base pair steps”.

Chem.Eur.Journal. (2006) 12, 2854-2865.

242) T.Meyer, C.Ferrer-Costa, A.Pérez, M.Rueda, A.Bidon-Chanal, F.J.Luque, C.A.Laughton and

M.Orozco. “Essential Dyanmics: A Tool for Efficient Trajectory Compression and Management”

J.Chem.Theor.Comput (2006) 2, 251-258.

243) M.Fuentes-Cabrera, P.Lipkowski, O.Huertas B.G.Sumpter, M.Orozco, F.J.Luque, J.C.Wells,

J.Leszczynski. “Aromaticity induced changes in the electronic properties of size-expanded DNA bases.

The case of xC”. International Journal of Quantum Chemistry. (2006), 106, 2338-2346.

244) A.Bidon-Chanal, M.Martí, A.Crespo, M.Milani, M.Orozco, M.Bolognesi, F.J.Luque and D.A.Estrin.

“Ligand-induced dynamical regulation of NO conversion in Mycobacterium Tubercolisis truncated-

hemoglobin-N. Proteins (2006). 64, 457-464.

245) C.Curutchet, M.Orozco, F.J.Luque, B.Mennucci and J.Tomasi “Dispersion and repulsion

contributions to the solvation free energy: Comparison of quantum mechanical and classical approaches

in the Polarizable Continuum Model”. J.Comp.Chem (2006). 27, 1769-1780.

246) J.Muñoz-Muriedas, X.Barril, J.M.López, M.Orozco and F.J.Luque “A hydrophobic similarity

analysis of solvation effects on nucleic acids” J.Mol.Mod., (2007) 13, 357-365.

247) I.Soteras, O.Lozano, A.Gómez-Esqué, C.Escolano, M.Orozco, M.Amat, J.Bosch and F.J.Luque

“On the Origin of Stereoselectivity in the Alkylation of Oxazolopiperidone Enolates”.

J.Am.Chem.Soc. (2006) 128, 6581-6588.


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248) J.R.Goñi, J.M.Vaquerizas, J.Dopazo and M.Orozco… “Exploring the reasons for the large density

of triplex-forming oligonucleotide target sequences in the human genome”. BMC Genomics. (2006) 7,

63-72. Selected for Faculty of 1000 Essentials

249) D.Talavera, A.Morreale, A.Hospital, C.Ferrer, J.L.Gelpi, X. de la Cruz, T.Meyer, R.Soliva,

F.J.Luque and M.Orozco. “A fast method for the determination of fractional contributions to solvation in

proteins”. Protein Science (2006) 15, 2525-2533.

250) J.R.Blas, J.M.López-Bes, M.Márquez, J.L.Sessler, F.J.Luque and M.Orozco “Exploring the

dynamics of Calix[4]pyrrole: The effect of solvent and fluorine substitution”. Chem.Eur.J. (2007), 13,

1108-1116.

251) C.Ferrer-Costa, M.Orozco and X de la Cruz “Characterization of compensates mutations in terms of

structural and physico-chemical properties” J.Mol.Biol. (2006), 365, 249-256.

252) M.Rueda, C.Ferrer, T.Meyer, A.Pérez, J.Camps, A.Hospital, J.L.Gelpí and M.Orozco. “A

consensous view to Protein Dynamics”. Proc. Natl. Acad. Sci. USA. (2007) 104, 796-801.

253) O.Huertas, J.Poater, M.Fuentes-Cabrera, M.Orozco, M.Sola and F.J.Luque. “Local aromaticity in

natural nucleobases and their size-expanded benzo-fused derivatives” J.Phys.Chem.A (2006) 110, 12249-

12258.

254) R.Soliva, J.L.Gelpi, C.Almansa, M.Virgili and M.Orozco. “Dissection of the recognition properties

of p38 MAP Kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor

family”. J.Med.Chem. (2007) 50, 283-293.

255) O.Carrillo and M.Orozco. “GRID-based molecular dynamics. A Tool for genomic-scale simulations

of channels in proteins”. Proteins. (2008) 70, 892-899.

256) Talavera, C.Vogel, M.Orozco, S.A.Teichmann and X de la Cruz. “ The (In)dependence ofalternative

splicing and gene duplication”. PLOS Comp.Biol. (2007) 3, 375-388. (Front Cover Article)

257) A.Noy, A.Pérez, C.Laughton and M.Orozco. “Theoretical study of large conformational transitions

in DNA: The B��A conformational change in water and ethanol/water”. Nucleic Acid Res. (2007) 35,

3330-3338.

258) M.Orozco, A.Noy, T.Meyer, M.Rueda, C.Ferrer, A.Valencia, A.Pérez, O.Carrillo, J.Fernández-

Recio, X de la Cruz and F.J.Luque. “Data mining of molecular dynamic trajectories of nucleic acids”. In


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“Computational Studies of RNA and DNA”. Challenges and Advances in Computational Chemistry and

Physics. Vol 2. J.Sponer and F.Lankas (Eds). Springer. Dordrecht. 2006. pp 121-146.

259) A.Pérez, I.Marchán, D.Svozil, J.Sponer, T.E.Cheatham, C.A.Laughton and M.Orozco.

“Refinement of the AMBER force-field for nucleic acid simulations. Improving the representation of

αααα////γγγγ conformations”. Biophysical Journal (2007) 92, 3817-3829. 261 Citations

260) M.Orozco, I.Marchán and I.Soteras. “Continuum analysis of conformational sampling in solution”.

In Continuum Solvation Models in Chemical Physics: Theory and Application”. B.Mennucci and

R.Cammi (Eds). Elsevier. Amsterdam, 2007. pp 499-522.

261) M.Rueda, P.Chacón and M.Orozco. “Thorough Validation of Protein Normal Mode Analysis- A

Comparative Study with Essential Dynamics”. Structure (2007), 15, 565-575.

262) D.Talavera, A.Hospital, M.Orozco and X de la Cruz. “A Procedure for the identification of

homologous alternative splicing events”. BMC. Bioinformatics. (2007), 8, 260-271.

263) I.Soteras, C.Curutchet, A.Bidon-Chanal, F.Dehez, J.Angyan, M.Orozco, C.Chipot and F.J.Luque.

“Derivation of distributed models of atomic polarizability for molecular simulations”.

J.Chem.Theor.Comp (2007), 3, 1901-1913.

264) F.Forti, X.Barril, F.J.Luque and M.Orozco. “Extension of the MST continuum solvation model to the

RM1 semiempirical Hamiltonian”. J.Comp.Chem (2007), 29, 578-587.

265) J.Fort, L.R. de la Ballina, H.E.Burghardt, C.Ferrer-Costa, J.Turnay, C-Ferrer-Orta, I.Usón,

A.Zorzano, J.Fernández-Recio, P.L.Fernández, M.Orozco, M.A. Lizarbe, I.Fita and M.Palacín. “Structure

of human 4F2hc ectodomain: crystallographic and in vivo evidence for homodimerization”. J.Biol.Chem.

(2007), 43, 31444-31452. PAPER OF THE WEEK

266) J.A.Ortega, J.R.Blas, M.Orozco, A.Grandas, E.Pedroso and J.Robles. “Binding affinities of

oligonucleotides and PNAs containing phenoxazine and G-clamp cytosine analogs are unusually

sequence-dependent”. Organic Letters. (2007). 9, 4503-4506.

267) A.Pérez, F.J.Luque and M.Orozco. “Entering molecular dynamics in the biological time scale.

Microsecond simulation of DNA”.J.Am.Chem.Soc. (2007), 129, 14739-14745.


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268) A.Aviñó, M.G.Grimau, M.Alvira, R.Eriitja, R.Gargallo, M.Orozco and C.Gonzales. “Triplex

formation using oligonucleotide clamps carrying 8-aminopurines”. Nucleoside, Nucleotides and Nucleic

Acids, (2007), 26, 979-983.

269) A.Noy, F.J.Luque and M.Orozco. “Theoretical Analysis of Antisense Duplexes: Determinants

of the RNase H Susceptibility”. J.Am.Chem.Soc. (2008), 130, 3486-3496.

270) A.Emperador, O.Carrillo, M.Rueda and M.Orozco. “Exploring the suitability of coarse-grained

techniques fort he representation of protein dynamics”. Biophysical Journal. (2008), 95, 2127-2138.

271) J.R.Goñi, A.Pérez, D.Torrents and M.Orozco. “Studying the role of DNA physical properties

on gene regulatory mechanisms in vertebrates”. Genome Biology 8, R263, 2007. Highly accessed

paper.

272) M.Orozco, A.Noy and A.Pérez “Recent advances in the study of nucleic acids flexibility by

molecular dynamics”. Curr. Op. Struct. Biol. (2008), 18, 185-193. April Front Cover Article.

273) A.Vázquez-Mayogoita, O.Huertas, M.Fuentes-Cabrera, B.G.Sumpter, M.Orozco and F.J.Luque. “Ab

initio study of naptho-derivatives of DNA bases”. J.Phys.Chem.B (2008) 112, 2179-2186.

274) A.Pérez, F.Lankas, F.J.Luque and M.Orozco. “Towards a consensus view of B-DNA

flexibility”. Nucleic Acids Res., (2008), 36, 2379-2394.

275) J.Gross, A.Aviñó, J.López de la Osa, C.González, L.Lacroix, A.Pérez, M.Orozco, R.Eritja and J.-L.

Mergny. “8-amino guanine accelerates quadruplex formation”. Chem.Com (2008) 2926-2928.

276) D.Svozil, I.Marchan, A.Pérez, T.E.Cheatham, F.Forti, F.J.Luque, M.Orozco, J.Sponer. “Geometrical

and electrostatic structure variability of the sugar-phosphate backbone in nucleic acids”. J.Phys.Chem.B.

(2008), 112, 8188-8197.

277) I.Soteras, C.Chipot, M.Orozco and F.J.Luque. “Induction in metal cation-benzene complexes”.

Phys.Chem.Chem.Phys. . (2008), 10, 2616-2624.

278) J.R.Goñi, C.Fenollosa, A.Pérez, D.Torrents, M.Orozco. “DNAlive: A tool for the physical analysis

of DNA at the genomic scale”. Bioinformatics. (2008), 95, 1731-1732.


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279) Xie,W.; Orozco,M*.; Truhlar,D*.; Gao,J*. “Molecular dynamics simulation of a 14281-atom system

with direct dynamics based on an explicit quantum mechanical all-atoms electronic wave function.

Polarization and charge redistribution in Bovine Pacreatic Trypsin Inhibitor in water”.

J.Chem.Theor.Comput. (2009), 5, 459-467. (highlighted as # 1 by the Journa).

280) Cozzini,P.; Kellogg,G.; Spyrakis,F.; AbrahamD.; Gabriele,C.; Emerson,A.; Fanelli,F.; Gohlke,H.;

Kuhn,L.; Morris,G.; Orozco,M.; Perthinhez,T.; Rizzi,M.; Sotriffer,C. “Target Flexibility”. J.Med.Chem.

(2008), 51, 6237-6255.

281) Bidon-Chanal,A.; López,J.M.; Orozco,M* and Luque,F.J*. “Thermodynamic analysis of the

hydration of neutral solutes”. In “Solvation Effects on Molecules and Biomolecules”. S.Canuto (ed).

Springer Science, B.V. 2008, pp103-113.

282) The BioMoby Consortiun, including Orozco,M. “Interoperability with Moby 1.0-It’s better than

sharing your toothbrush”. Brieffings in Bioinformatics. (2008), 9, 230-231.

283) Soteras,I.; Lozano,O.; Escolano,C.; Orozco,;M.; Amat,M.; Bosch,J and Luque,F.J. “Structure-

directed reversion in the p-facial stereoselective alkylation of chiral bicyclic lactams”. J.Org.Chem

(2008), 73, 7756-7763.

284) Meyer,T.; de la Cruz,X and Orozco,M. “An atomistic view to the gas phase proteome”. Structure.

(2009), 17, 88-95.

285) Emperador,A.; Meyer,T.; Orozco,M. “United-atom discrete molecular dynamics of proteins using

physics-based potentials”. J.Chem.Theor.Comput., (2008), 4, 2001-2010.

286) Klamtz,A.; Mennucci,B.; Tomasi,J.; Barone,V.; Curutchet,C.; Orozco,M.; Luque,F.J. "On the

performance of continuum solvation methods. A comment on Universal Approaches to Solvation

Modeling". Acc.Chem.Res., (2009), 42, 489-492.

287) Bidon-Chanal,A.; Huertas,O.; Orozco,M*.; Luque,F.J*. “Solvation enthalpies of neutral solutes in

water and octanol”. Theor.Chem.Acc. (2009), 123, 11-20.

288) Velázquez-Muriel,J.A.; Rueda,M.; Isabel,C.; Pascual-Montano,A.; Orozco,M*.; Carazo,J.M*.

“Comparison of molecular dynamics and superfamily spaces of protein domain deformation”. BMC

Struct. Biol., (2009), 9,6-20 .


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289) J. Camps, O. Carrillo, A. Emperador, L. Orellana, A. Hospital, M. Rueda, D. Cicin, M. D’Abramo,

J.L. Gelpí and M.Orozco. “FlexServ: An integrated tool for the analysis of protein flexibility”.

Bioinformatics (2009), 25, 1709-1710.

290) I.Soteras, F.Forti, M.Orozco* and F.J.Luque*. “Performance of the IEG-MST solvation continuum

mode in a blind test prediction of hydration free energies”. J.Phys.Chem.B. (2009), 113, 9320-9334.

291) H.Saneyoshi, S.Mazzini, A.Aviñó, G.Portela, C.González, M.Orozco, V.E.Marquez and

R.ERitja. “Conformationally Rigid Nucleoside Probes Help Understand the Role of Sugar Pucker

and Nucleobase Orientation in the Thrombin Binding Aptamer”. Nucleic Acids Res., (2009), 37,

5589-5601.

292) M.D’Abramo, T.Meyer, P.Bernadó, J.Fernandez-Recio and M.Orozco. “On the use of low resolution

data to improve structure predictions of proteins and protein complexes”. J.Chem.Theor.Comput. (2009),

5, 3129-3137.

293) R.Garcia-Fandiño, J.Granja, M.D’Abramo and M.Orozco. “Theoretical Characterization of

the dynamic behaviour and transport properties of α,γ− α,γ− α,γ− α,γ−peptide nanotubes in solution”.

J.Am.Chem.Soc. (2009), 131, 15678-15686.

294) A.Noy, I.Soteras, F.J.Luque and M.Orozco. “The impact of monovalent ion force-field model in

nucleic acids simulations”. Phys.Chem.Chem.Phys. (2009), 11, 10596-10607.

295) Eva Fadrná, Naďa Špačková , Joanna Sarzyñska, Jaroslav Koča, Modesto Orozco, Tomas E.

Cheatham III and Jiří Šponer. “Single stranded loops of quadruplex DNA as key benchmark for testing

nucleic acids force fields”. J.Chem.Theor.Comput (2009), 5, 2514-2530.

296) I.Faustino, A.Aviño, I.Marchán, F.J.Luque, R.Eritja and M.Orozco. “The Unique tautomeric

and recognition properties of thio-thymines?”. J.Am.Chem.Soc., (2009), 131, 12845-12853

297) A.Vázquez-Mayagoitia, O.Huertas, G.Brancolini, B.G.Sumpter, M.Orozco, F.J.Luque, R.di Felici

and M.Fuentes-Cabrera. “Ab initio study of structural, tautomeric, pairing and electronic properties of

seleno-derivatives of thymine”. J.Phys.Chem.B. (2009), 113, 14461-14472.

298) R.Lavery, K.Zakrzewska, D.Beveridge, T.C.Bishop, D.Case, T.Cheatham III, S.Dixit, B.Jayaram,

F.Lankas, C.Laughton, J.H.Maddocks, A.Michon, R.Osman, M.Orozco, A.Pérez, N.Spackova, J.Sponer.


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“A systematic molecular dynamics study of the nearest-neighbor effects on base pair and base step

conformations and fluctuations in B-DNA”. Nucleic Acids Res. (2010), 38, 299-311.

299) J.Watts, N.Martín-Pintado, I.Gómez-Pinto, G.Portella, M.Orozco, C.González and M.Dhama.

“Structure and stability of FANA-RNA and ANA-RNA hy brid duplexes”. Nucleic Acids Res.,

(2010), 38, 2488-2511. Selected for Faculty of 1000 essentials.

300) E.M.Novoa, M.Castro, M.Orozco and L.Ribas de Pouplana. “A genomic method to indentify

pathogenicity-related proteins. Application to aminoacyl-tRNA sythentase-like proteins”. FEBS Lett.,

(2010), 584, 460-466.

301) A.Aviñó, E.Cubero, R.Gargallo, C.González, M.Orozco and R.Eritja. “Structural Properties of G.T-

parallel duplexes carrying 8-aminopurine residues”. J.Nucleic Acids. (2010). Article ID 7636658, 1-11.

302) C.A.Laughton, M.Orozco. “Nucleic Acid Themed Issue. Editorial”. Phys.Chem.Chem.Phys. (2009),

11, 10541-10542.

303) F.Raimondi, M.Orozco* and F.Fanelli*. “Deciphering the deformation modes associated with

function retention and specialization in members of the Ras Superfamily”. Structure. (2010), 18,

402-414. Highleted by A.W.. van Wynsberghe and Q.Cui. pp 281-282 same issue.

304) A.Emperador, T.Meyer and M.Orozco. “Study of protein flexibility form discrete molecular

dynamics simulations using quasi-physical potentials”. Proteins (2009), 78, 83-94.

305) I.Soteras, M.Orozco and F.J.Luque. “Performance of the IEF-MST Solvation Continuum Model in

the SAMPL2009 Blind Test Prediction of Hydration and Tautomerization Free Energies”. J.Computer

Aided Mol.Design. (2010), 24, 281-291.

306) A.Pérez and M.Orozco. “Real time atomistic description of DNA unfolding”. Angew. Chem. Int.

Ed. Eng. (2010), 49, 4805-480

307) I.Faustino, A.Pérez and M.Orozco. “Towards a Consensus view of duplex RNA flexibility?”.

Biophysical Journal. (2010), 99, 1876-1885.

308) S.Pettifer and the EMBRACE and INB-consortia including M.Orozco. “The EMBRACE web service

collection”. Nucleic Acids Res. (2010). 38, W683-W688.


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309) T.Meyer, M.D’Abramo, A.Hospital, M.Rueda, C.Ferrer-Costa, A.Pérez, O.Carrillo,

C.Fenollosa, D.Repchevsky, J.L.Gelpí and M.Orozco. MoDEL (Molecular Dynamics Extended

Library). A database of atomistic molecular dynamics simulations”. Structure. (2010). 18, 1399-

1409.

310) L.Orellana, M.Rueda, C.Ferrer-Costa, J.R.López-Blanco, P.Chacón and M.Orozco. “Approaching

elastic network models to atomistic molecular dynamics”. J.Chem.Theor.Comput. (2010). 6, 2910-2923.

311) C.Pons, M.D’Abramo, D.I.Svergun, M.Orozco, P.Bernadó and J.Fernández-Recio. “Structural

characterization of protein-protein complexes by integrating computational docking with small-angle

scattering data”. J.Mol.Biol (2010). 403, 217-230.

312) G.Portella and M.Orozco. “Multiple routes characterize the folding of a small DNA hairpin”.

Angew. Chem. Int. Ed. Eng. (2010), 49, 7673-7676.

313) F.J.Luque, F.Dehez, C.Chipot and M.Orozco. “Polarization effects in molecular interactions”. WIREs

Comput.Mol.Sci. (2011) 1, 844-854.

314) E.M.Novoa, L.Ribas de Pouplana, X.Barril and M.Orozco. “Ensemble docking from homology

models”. J.Chem.Theor.Comput. (2010), 6, 2547-2557.

315) F.Raimondi, G.Portella, M.Orozco and F.Fanelli. “Nucleotide switches the information flow in Ras

GTPases”. PLOS Comput.Biol., (2011) 7(3), e1001098, 1-17

316) Banás,P.; Hollas,D.; Zgarbová, Jurecka,P.; Orozco,M.; Cheatham,T.E.; Sponer,J.; Otyepka,M.

“Performance of molecular mechanics force-fields for RNA simulations. Stability of UUCG and GNRA

hairpins”. Journal Chemical Theory & Comput., (2010) 6, 3836-3849.

317) C.Pons, D.Talavera, X. de la Cruz, M.Orozco and J.Fernández-Recio. “Scoring by intermolecular

pairwise propensities of exposed residues (SIPPER): A new efficient potential for protein-protein

docking”. J.Chem.Inf.Mod. (2011) 51, 370-377.

318) A.Ayuso-Tejedor, R.García-Fandiño, M.Orozco, J.Sancho and P.Bernadó. “Structural analysis of an

equilibrium folding intermediate in the apoflavodoxin native ensemble by small X-ray scattering”.

J.Mol.Biol. (2011). 406, 604-619.

319) M.Orozco, L.Orellana, A.Hospital, A.N.Naganathan, A. Emperador, O.Carrillo and J.L.Gelpí.

“Coarse Grained Representation of Protein Flexibility. Foundations, successes and shortcomings”. In


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“Computational Chemistry Methods in Structural Biology". Advances in Protein Chemistry and

Structural Biology, vol 85. Ed. C.Christov. Burlington. Academic Press, 2011, pp 183-215 (CL)

320) Kowalczyk,L., Ratera,M., Paladino,A., Bartoccioni,P., Errasti,E., Valencia,E., Portella,G.,

Bial,S., Zorzano,A., Fita,I., Orozco,M., Carpena,X., Vázquez-Ibar,J.L, Palacín,M.” Molecular basis

of substrate-incuded permeation by an aminoacid antiporter”. Proc. Natl. Acad. Sci. USA, 108,

3935-3940 (2011).

321) M.D’Abramo, M.Orozco and A.Amadei. “Effects of local electric fields on the redox free energy of

single stranded DNA”. Chemical Communications (2011), 47, 2646-48.

322) S.Djebali, J.Lagarde, P.Kapranov, V.Lacroix, C.Borel, J.M.Mudge, C.Ucla, S.Foissac, C.Howald,

J.Chrast, P.Ribeca, D.Martin, R.R.Murray, X.Yang, L.Ghamsari, C.Lin, I.Bell, E.Dumais, J.Drenkow,

M.Tress, JL.Gelpí, M.Orozco, A.Valencia, N.L. van Berkum, B.R.Lajoie, M.Vidal,

J.Stamatoyannopoulos, J.Harrow, T.Hubbard, J.Dekker, A.Frankish, K.Salehi-Ashtiani, A.Reymond,

S.E.Antonarakis, R.Guigó and T.R.Gingeras. “Evidence for transcript networks composed of chimeric

RNAs in human cells”. PLOS One. In Press. 2011.

323) A.Stein, M.Rueda, A.Panjkovich, M.Orozco* and P.Aloy*. “A systematic study of the energetics

involved in structural changes upon association and connectivity in protein-protein interaction networks”.

Structure (2011), 19, 881-889.

324) Puente,X.S.; Pinyol,M.; Quesada,V.; Conde,L.; Ordóñez,G.R.; Villamor,N.; Escaramis,G.; Jares,P.;

Bea,S.; González-Diaz,M.; Bassaganyas,L.; Baumann,T.; Juan,M.; López,M.; Colomer,D.; Tubío,J.C.;

López,C.; Navarro,A.; Tornador,C.; Aymerich,M.; Rozman,M., Hernández,J.M., Puente,D.A.;

Freije,J.M.; Velasco,G.; Gutiérrez-Fernández,A.; Costa,D.; Carrió.A.; Guijarro,S.; Enjuanes,A.;

Hernández.L.; Yagüe,J.; Nicolas,P.; Romeo-Casabona,M.; Himmelbaure,H.; Dohm,J.; de Sanjosé,S.;

Piris,M.A.; de Alava,E.; San Miguel,J.; Royo,R.; Gelpí,J.L.; Torrents,D.; Orozco,M.; Pisano,D.G.;

Valencia,A.; Guigó,R.; Bayes,M.; Heath,S.; Gut,M.; Klatt,P.; Marshall,J.; Raine,K.; Stebbings,L.A.;

Futreal,P.A., Stratton,M.R.; Campbell,P.J.; Gut,I.; López-Guillermo,A.; Estivill,X.; Montserrat,E.;

López-Otín,C.; Campo,E. “Whole-genome sequencing identifies recurrent mutations in chronic

lymphocytic leukaemia”. Nature (2011) 475, 101-105.

325) A.Naganathan, M.Orozco. “The protein folding transition-state ensemble from a Go-Model”.

Phys.Chem.Chem.Phys. (2011) 13, 15166-15174.

326) O.Flores and M.Orozco. “NucleR: a package for non-parametric nucleosome positioning”. “NucleR:

a package for non-parametric nucleosome positioning”. Bioinformatics (2011) 27, 2149-2150.


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327) A.Naganathan and M.Orozco. “The native ensemble and folding of a protein molten-globule.

Functional consequence of downhill folding”. J.Am.Chem.Soc. (2011) 133, 12154-12161.

328) J.R.Blas, O.Huertas, C.Tabares, B.G.Sumpter, M.Fuentes-Cabrera, M.Orozco, P.Ordegón and

F.Javier Luque. “Structural, dynamic and electronic transport properties of modified DNA duplexes

containing size-expanded nucleobases”. J.Phys.Chem.A 115, 11344-11354 (2011).

329) O.Deniz, O.Flores, F.Batistini, A.Pérez, M.Soler-López and M.Orozco. “Physical properties of naked

DNA signal gene regulatory regions”. BMC Genomics. 12:489 (2011).

330) A.Pérez, F.J.Luque and M.Orozco. “Frontiers in molecular dynamics simulations of DNA”.

Acc.Chem.Res., ASAP, DOI: 10.1021/ar2001217

331) V.Quesada, L.Conde, N.Villamor, G.Ordóñez, P.Jares, L.Bassaganyas, A.J.Ramsay, S.Beà,

M.Pinyol, A.Martínez, M.López-Guerra, D.Colomer, A.Navarro, T.Baumann, M.Aymerich, M.Rozman,

J.Delgado, J.M.Hernández, M.González-Díaz, D.A.Puente, G.Velasco, J.M.Freire, J.M.C. Tubío,

R.Royo, Josep L. Gelpí, M.Orozco, D.G.Pisano, J.Zamora, M.Vázquez, A.Valencia, H.Himmelbauer,

M.Bayés, S.Heath, M.Gut, I.Gut, X.Estivill, A.López-Guillermo, X.S.Puente, E.Campo, C.López-Otín.

Nature Genetics In Press. 2011.


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INVITED CONFERENCES

“Beyond the MEP. New approaches for the theoretical study of biochemical systems”. Research seminars. Boehringer Ingelheim Research Center. Danbury. CT. USA. 1993. “New approaches for force-field parametrization. The importance of the environment”. Organic Chemistry Conferences. Yale University. New Haven. CT. USA. 1993. ” Mecanismo de acción de la FK506 binding protein”. Ciclo de seminarios de bioquímica estructural. Consejo Superior de Investigaciones Científicas. Barcelona. Spain. 1993. ” Introducción del efecto del solvente en biomoléculas. Implementación en MOPAC. X Reunión del grupo de Química Cuántica de Cataluña Barcelona. Spain. 1994. “La Bioquímica teórica una herramienta para la investigación en farmacia”. Ciclo de seminarios de investigación. Facultad de Farmacia. Universidad de Barcelona. Barcelona. Spain. 1994. “Supercomputing applied to the study of biochemical systems”. Short Course of high performance computing. Centre de Supercomputació de Catalunya. Barcelona. Spain. 1994. “Molecular Dynamics and Free Energy Perturbation studies of the interaction between drugs and proteins”. Workshop on Computational Approaches in the analysis and engineering of proteins. Fundación Juan March. Madrid. Spain. 1994.

“Short course on theoretical methods for the calculation of free energy differences”. Boehringer Ingelheim Research Center. Danbury. CT. USA. 1995. “Approaches to the introduction of solvent effects in chemical and biochemical processes” CECAM Workshop. Lyon. France. May 1995. “Estrategias para la incorporación del efecto del solvente XI Reunión del grupo de Química Teórica de Cataluña Barcelona. Spain. 1995. ”Nuevas aproximaciones de dinámica molecular para el estudio de interacciones biomoleculares en proteínas y ácidos nucleicos” CESCA “Curso monográfico de modelización molecular” Barcelona. Spain. June 1995. “L’efecte del solvent en el reconeixement molecular a la bioquímica” XII Reunión del grupo de Química Teórica de Cataluña Tarragona. Spain. 1996.


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“Molecular Dynamics in Biological systems” Jornades de la Mediterrania Menorca. Spain 1996. “Molecular Modeling of the recognition mechanism of xanthine oxydase” XXIII QTEL Congress. Caceres. Spain 1996. “Modelado Teórico de la triple hélice de DNA” Cicle de Conferencies Ciencia i Societat Universitat de les Illes Balears. Mallorca. Spain 1996. ”El efecto del solvente en sistemas químicos y bioquímicos” Seminarios de Investigación. Instituto de Química Orgánica General CSIC Madrid. Spain 1997. “Triplex DNAs as potential drugs”. Boehringer Ingelheim Research Center. Danbury. CT. USA. 1997. “Generalization of the Molecular Electrostatic Potential for the study of molecular interaction”. 214th American Chemical Society National Meeting Invited Speaker Las Vegas. USA 1997 “Temas recientes de estructura de ácidos nucleicos”. Invited lecture Col.legi de Doctors i Llicenciats de Catalunya. Barcelona 1998. “La dinámica molecular en el estudio de macromoléculas” Invited lecture “Departamento de Química Orgánica” Universidad de Santiago de Compostesla Santiago de Compostela. 1998 “MD simulations of anamalous DNA structures” Invited lecture “Departament of Pharmaceutical Sciences” University of Nottingham Nottingham. UK 1998. “Use of SCRF methods in Drug Design” Invited Conference “QSAR´98 Copenhagen. Denmark 1998 “Molecular Dynamics studies of DNA triple helices Invited Conference IQSP President´s meeting Elba. Italy 1998 “La Dinámica Molecular: Una herramienta útil en el estudio de ácidos nucleicos?” Invited lecture Seminarios del Instituto de Estructura de la Materia. CSIC Madrid 1998.


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“MD simulation of unusual DNA structures” Invited Lectures 7rh Conference on Current Trends in Computational Chemistry Jackson Mississippi, USA 1998. “New appraoches for the representation of molecular interactions in biochemical systems” Conferencia Invitada Research seminars. Boehringer Ingelheim Research Center. Danbury. CT. USA. 1998. “Formas unusales del DNA. Una aproximación teórica”. Invited lecture CNB-Cycle of research conferences CNB Centro Nacional de Biotecnología Madrid 1998. ”New methodological approaches to the study of bioorganic systems in solution” Invited lecture Czech Academia of Science Praga. Czech Republica 1999. “MD Simulations of Anomalous DNA Structures” Invited conference Biochemistry and Molecular Biology’99 American Society for Biochemistry and Molecular Biology San Francisco. USA 1999. Molecular Dynamics simulations of nucleic acid structures” Invited lecture Department of Pharmaceutical Chemistry Pharmacy School University of California San Francisco San Francisco. USA 1999 Theoretical studies of anomalous nucleic acids” Invited lecture Department of Molecular Biology The Scripps Research Institute La Jolla. USA 1999 “Hacia la expansión del código genético” Conferencia Invitada II RANN El Escorial. 1999. “Métodos teóricos en el diseño Molecular” Invited conference Uriach i Cia Barcelona 2000. “Simulaciones de formas inusuales del DNA” Invited conference CID-CSIC.


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Barcelona 2000. “Metodos teóricos en el estudio de sistemas bioorgánicos” Invited conference Departament de Química Orgánica Universitat de Barcelona Barcelona 2000 “Study of anomalous forms of DNA. Can simulation provide useful results?” Invited conference Minnesota University Minneapolis 2000. “Recent developments for the representation of solvent effects in drug design” Invited conference Boehringer Research Center Danbury. CT. 2000 “Modelización Molecular en Diseño de Fármacos”. Plenary lecture I Jornadas de Bioinfromática Cartagena. 2000 “Molecular Dynamics Simulations of Anomalous forms of DNA” Invited Conference EUCO-CC3 Budapest. 2000. “ Estudio teórico de sistemas biomoleculares ” Plenary conference Beckman Coulter. XXIII Congress of Spanish Biochemistry Society. Granada 2000. “Molecular Dynamics Simulations of DNA structures” Invited Conference Chemistry Department ETH Zurich. 2001 “New challenges in drug design ” Invited conference Workshop on Structural Genomics and Bioinformatics Fundación Juan March Madrid. 2001 “Going beyond structure. Can theory help?” Invited conference Department of Structural Chemistry Cambridge University Cambridge. 2001 “El DNA- Una visión dinámica” Invited Conference “International Workshop on modeling of chemical and biochemical molecules” Fundación Ramón Areces


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Madrid. 2001 “Aproximaciones teóricas al estudio de proteínas. Una visión dinámica” Invited conference “Ciclo de Conferencias en Bioquímica” Universitat Autònoma de Barcelona Barcelona. 2001 “The diffuse molecular modeling scenario” Invited Conference Boehringer Conference Danbury CT. USA 2002 “ Current challenges in molecular modelling” Invited lecture Rockefeller University NY. USA 2002 “Prespectives in modelling and Bioinformatics” Invited Conference Yale University CT. USA 2002. -“ Simulations of anomalous DNA structures” Invited Cofnerence ISQBP President meeting Snowbird Utah. USA 2002. “Discovering new aspects of Nucleic acids through molecular simulations” Invited Lecture Upsala University Sweden. 2003 “Simulations of anomalous forms of DNA” Invited Conference Workshop on simulation of nucleic acids Bernoulli Center Laussane Switzerland 2003 “Solvation in biomolecular systems” Invited Conference XI International Congress of Quantum Chemistry Bonn Germany, 2003 “Simulación de ácidos nucleicos” Invited Conference Monográfico 50 años del descubrimiento del DNA. Curso de Verano de El Escorial. El Escorial. Madrid. 2003 “New Challegens in Drug Design” Invited Lecture


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Meeting of the European Society of Screening Madrid 2003. “Fronteras en el descubrimiento de fármacos” Conferencia Plenaria Semana de la Ciencia Universidad San Pablo CEU Madrid. “Frontiers in the simulation of nucleic Acds” Conferencia Plenaria ISQBP- President Meeting Como. Italy 2004. “New advances in the treatment of solvation” Conferencia Invitada International meeting on quantum chemistry. In honor to Prof. Tomasi Luca. Italy 2004. “Explorando el genoma para el diseño de nuevas bioterapias” Conferencia Invitada Cursos de Verano de la Universidad de Málaga Ronda. 2004 “Simulaciones de DNA y diseño de nuevas estrategias terapéuticas” Conferencia Invitada XXI Congreso de la SEBBM. Lleida 2004. “Exploring DNA for the design of new therapies” Conferencia Invitada Structural Biology of Cancer Targests Centro Nacional de Investigaciones Oncológicas Madrid. 2004. “Exploring the flexibility of nucleic acids” Invited conference Cornell University New York 2004. “ Solvation from small molecules to Proteins” Invited Conference Bill Jorgensen’s Symposium. Yale University 2005 “ Unusual DNA structures” Invited Conference Weslayan University, 2005 “Nucleic acids flexibility from Molecular Dynamics simulations” Invited Conference XIV Conversations of Biomolecular structure SUNY at Albany. New York 2005 -“Solvent effects in chemical and biochemical systems”


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Chairman X International Conference of Theoretical Physics New Orleans, 2005 -“Una visió teórica dels sistemes bioquímics” Jornades de Supercomputació (JOCS05) Tarragona, 2005 -“Estudio teórico de sistemas biomoleculares” Invited Speaker XXX Reunión Bienal de la Real Sociedad de Química Lugo, 2005 -“ MD simulations in the post-genomic era” Plenary lecture FEBS-Course on “Theoretical modeling of ligand binding and enzyme catalysis” Tromso. Norway, 2005 -“ De la química cuántica a la bioinformática.” Conferencia Plenaria Jornadas de Ciencia Facultad de Ciencias Universidad de Málaga Málaga 2005 “Molecular Dynamics simulations in the postgenomic era” Conferencia plenaria Ciclo conferencias del CIB. Madrid 2006 “DNA in hostile environments” Plenary lecture Euresco Conference Trest. Czech Republica. 2006 -“El diseño racional de biomoleculas” Plenary lecture Cursos Verano de U.Málaga Málaga 2006. “A new paradigm for molecular dynamics simulations of macromolecules” Plenary lecture (distinguished lecturer) CCSBp meeting Nottingham. UK 2007 “The importance of flexibility in drug design. A molecular dynamics prespective” Plenary lecture From Structural Genomics to Drug Discovery Parma. Italy. 2008 “Genome scale protein simulation” CASP7.5 Meeting Madrid. 2008 - “DNA from quantum chemistry to genomics”


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Beckman seminary University of Illinois at Urbana Champaign Illinois. USA. 2008. - “Theoretical Studies on DNA from quantum chemistry to genomics” Gordon Conference on Computational Chemistry Mount Holyoke. Massachussets. USA. 2008. - “Dynamics aspects of protein structure and interactions” EMBO Course of Protein-Protein docking Barcelona, Spain. 2008 - “El papel de la supercomputación en Biomedicina”. Instituto Roche-Fundación Bamberg Barcelona, Spain. 2009 - “DNA from atoms to genomics” Biomolecular Simulations Stockholm. Sweden. 2009. -“Computational and Medicinal Chemistry” American Chemical Society Meeting Washington DC. 2009 - “Grand Challenges in Computational Biology. In and out of the grid problems” EGEE’09 Conference Barcelona 2009 - “New computational challenges in Biology”. EGEE’10 User Conference. Upsala. Sweden 2010. - “Computational challenges in Life Sciences”. HPC-Prace meeting Julich. Germany 2010. - “Exploring DNA folding and unfolding from molecular dynamics simulations” Symposium on nucleic acid chemistry, structure and interactions Nova Gorica, Slovenia 2010. - “Biomolecular simulations. An overview”. Brucket Plenary Lecture. IV Spanish Portuguese Biophysical Congress. Zaragoza. 2010. - Challenges in molecular dynamics of macromolecules”. EMBO Course on Molecular Modeling. Paris. 2010. - “Datamining in cancer genome projects. Why a supercomputer center is needed?”. III International Symposium on Biomedical Informatics in Europe. San Sebastian. 2010. - “DNA from atom to chromosome”. Annual series of invited conferences at the Institute for Personalized Medicine.


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Barcelona 2011. - “The journey of a computational chemist along DNA”. International meeting of the World Association of Theoretically Oriented Chemist (WATOC). Santiago de Compostela. 2011. - “DNA, from quantum chemistry to bioinformatics”. Telluride Meeting on RNA. Telluride. Colorado. USA - The impact of methylation on the physical properties of DNA”. “Coarse-Grain Mechanics of DNA”. CECAM Conference Lausanne, Switzerland. 2011 - “On Silico Navigation in the DNA world” Modeling Interactions in Biomolecules V Kutná Hora, Czech Republic. 2011 - “New approaches to represent protein dynamics” CPMD International Congress Barcelona 2011 - “Protein dynamics in the post-genome era” CECAM workshop “Combining experimental and computational techniques to study protein behavior” Lugano, Italy 2011-11-03 - “EESI Final Exascale Conference” E-Sciences in Exascale computers Meeting Barcelona 2011 - “Pushing the frontiers of molecular dynamics simulations” Biomed Conference on Protein Dynamics Barcelona 2011. - “Molecular dynamics in the postgenome scenario” Fribourg Universtiy Conference Series Fribourg. Germany 2011


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ORGANIZATION OF COURSES AND CONFERENCES Chairman of session in the XII reunión del Grupo de Química Teórica de Cataluña. Tarragona 1996

Organizer of the international workshop “molecular modeling of solvation in biochemical systems”. Barcelona 1996.

Organizer of the workshop “computational techiques for the modeling and design of bioactive molecules”. Barcelona

1997.

Organizer of the workshopt “use of data bases in drug design”. Barcelona 1997.

Session chairman of the symposium “Role of electrostatics in chemistry”. ACS Meeting. Las Vegas. USA. 1997.

Session chairman of the symposium “Combined Quantum Mechanical/Molecular Mechanical Methods”. ACS

Meeting. Las Vegas. USA. 1997.

Organizer of the workshop “El fàrmac de la natura al laboratori”. Els Juliols de la UB. Barcelona. 1998.

Session chairman of the ISQBP President´s meeting. Elba. Italy 1998.

Organizer of the Meeting of the Theoretical Molecular Biology group of the Spanish Bochemical Society. Navarra

1999.

Member of the Organizing Comittee of the “Jornades Catalanes de Supercomputació”. Barcelona 1999.

Member of the Organizing Comittee of the “Segones Jornades de Modelització Molecular”. Barcelona 1999.

Organizer of the conference series: “Bioinformática 2000 y Bioinformática 2001”. Parc Científic de Barcelona. 2000-2001. Chairman of the session: “Proteómica Estructural”. “Segundas Jornadas Españolas de Bioinformática”. Malaga 2001. Organizer of the conference: “Perspectives in Structural Bioinformatics”. Barcelona. 2002 Organizer of the II Meeting of the Catalonian Network of Bioinformatics. Lleida 2003. Organizer of the Meeting of the Spanish Bioinformatic Network. Zaragona 2006 Organizer of the “Grand Challenges in Compuational Biology”. Barcelona 2008 Organizer of the “Joint EBI-INB Hands on Meeting on Bioinformatics”. Barcelona 2008. Organizer of the “Joint CCPB-INB Hands on Meeting on Biosimulation”. Barcelona 2008. Organizer of the “Joint IRB-BSC on expanding the frontier of MD simulations”. Barcelona 2009 Organizer of the “CAPRI meeting 2009”. Barcelona 2009 Organizer of the “Joint IRB-BSC on Exascale Challenges in Computational Biology”. Barcelona 2010 Coorganizer of the “ICREA conference on network medicine approached to human disease”. Barcelona 2011.


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ADDITIONAL INFORMATION

Associated Editor Wiley Intersdiciplinary Reviews on Computational Molecular Science.

Advisory editor of Theoretical Chemistry Accounts: Theory, Computation and Modeling

Member of the Editorial board of Journal of Computational Chemistry

Member of the Editorial board of Journal of Chemical Theory and Computation

Member of the Editorial Board of Physical Chemistry Chemical Physics

Member of the Editorial Board of Journal of Molecular Recognition

Counselor of the International Society of Quantum Biology and Pharmacology

Member of the Scientific Committee of the PRACE (Partnership for advanced computing in Europe)

Referee of (among others): J.Org.Chem., Int.J.Biol.Macromol., Macromolecules, Biophysical Chemistry,

J.Comp.Chem., J.Chem.Inform.&Comp.Science, JCTC, J. Med. Chem., J,Mol.Graph&Mod., J.Biomol.Struct.&Dyn.,

Chemical Physics, Biochemistry, FEBS Letters, Bioinformatics, J.Phys.Chem., J.Chem.Phys., .Chem.Chem.Phys,

BMC Structural Biology, J.Phys.Org.Chem., J.Mol.Struct(Theochem), J.Am.Chem.Soc, Biophysical Journal,

Chemical Reviews, Angew. Chem., Chem.Soc. Rev., Proc. Natl. Acad. Sci , USA, Nature Methods and Science.

Referee of the Spanish Science Foundation (ANEP), Agencias de evaluación Andalucia y Catalunya, National Science

Foundation (NSF), Austrian Science Foundation, French Science Foundration, German Science Foundation, Argentina

Science Foundation, COLOCIENCIAS, and Czech Science Foundation, Referee of projects for the European Union

Advisor of the Philip Morris External Research Program

Coordinator of the Catalonian Network of Biomolecular Modeling. Coordinator of the Group of Theoretical Molecular

Biology of the Spanish Society of Biochemistry and Molecular Biology.

Consultant of Boerhinger Ingelheim Pharmaceutical, Inc. USA., Almirall Prodesfarma. Barcelona. Spain

Uriach & Cia. Barcelona. Spain, PalauPharma. Barcelona. Spain, Kraft, Inc. USA, Pfizer Inc. Mass. USA.

Consultant of the “Subdirección General de Planificación y Seguimiento”. Spanish Ministry of Science and

Technology. 2002-2004 Member of the Panel of Experts of the Ministry of Science and Technology in the evaluation

of Biomedicine projects. 2003. Member of the Evaluation Panel of the Program Ramon & Cajal. 2003-2008. Member

of the Evaluation Panel of the Program Juan de la Cierva. 2004-2008. Member of the Panel of Experts of the Ministry

of Science and Technology in the design of the General Research Plan for 2004-2007. Area of Biotechnology.

Coordinator of the Computational and Structural Biology panel of the Spanish Evaluation Agency.

PERSONAL DATA · National annual award for young scientists of the Spanish Society of Biochemistry...

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Transcript of PERSONAL DATA · National annual award for young scientists of the Spanish Society of Biochemistry...