Removal of the 1st order Rayleigh scatter effect Åsmund Rinnan.
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Transcript of BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and...
![Page 1: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/1.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
QxPR methods in biomedicine – effect of geometry optimization
Åsmund Rinnan
![Page 2: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/2.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
QSxR?! QSAR?? QSPR!?
• Quantitative• Structure• Activity or
Property• Relationship
Estrogen -receptor
![Page 3: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/3.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
Basics of QSxR
2D 3D
O
OHO
OH
![Page 4: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/4.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
Basic of QSxR3D Descriptors
MW: 270.241Dipole: 3.44SASA: 470.87FISA: 182.33PISA: 288.54Volume: 795.13DonorHB: 2AccptHB: 3.75Dip^2/V: 0.0149Ac*DN^.5/SA: 0.0113
![Page 5: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/5.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
Basic of QSxR3D Descriptors
MW: 270.241Dipole: 3.44SASA: 470.87FISA: 182.33PISA: 288.54Volume: 795.13DonorHB: 2AccptHB: 3.75Dip^2/V: 0.0149Ac*DN^.5/SA: 0.0113
![Page 6: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/6.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
Basics of QSxRDescriptors PLS
B
And the rest is chemometrics…
Attributeof interest
![Page 7: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/7.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
Geometry optimizationBasics
O
OHO
OH
days
sec
min
h
![Page 8: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/8.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
Accuracy vs. Time
UFF
AM1
PM3 HF
B3LYP
Mechanical Semi-empiricalDensity
FunctionalTheorem
Time consumption
Seconds Days
Theoretical level
IntroductionQuestionStudyResultsSummary
MM3*
![Page 9: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/9.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
Accuracy vs. Time
UFF
AM1
PM3 HF
B3LYP
Mechanical Semi-empiricalDensity
FunctionalTheorem
Time consumption
Seconds Days
Theoretical level
IntroductionQuestionStudyResultsSummary
MM3*
1 80Dielectric constant
![Page 10: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/10.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
Accuracy vs. Time
UFF
AM1
PM3 HF
Mechanical Semi-empiricalDensity
FunctionalTheorem
Time consumption
Seconds Days
Theoretical level
IntroductionQuestionStudyResultsSummary
MM3*
6-31g(d,p)
Basis setsSTO-3g
6-31gB3LYP
![Page 11: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/11.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
DataDatasets
O
OHO
OH
IsoflavonoidsOH
Aglycons
Estrogen like
compounds
![Page 12: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/12.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
O
O
OH
Isoflavonoids
Estrogen like
compounds
DataProperties
Melting point
![Page 13: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/13.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
DataProperties
OHAglycons
log P
![Page 14: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/14.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
DataOverview
UFF
AM1
PM3
HF
B3LYP
MM3*
Meltin
g p
oin
tlo
g P
x 2
x 3
x 3
![Page 15: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/15.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
DataDescriptors
![Page 16: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/16.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
MethodsValidation
Leave-one out cross-validation
![Page 17: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/17.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
MethodsVariable selection
Variable selection:• Jack-knifing• Principal variables
![Page 18: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/18.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
ResultsDescriptor package
![Page 19: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/19.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
ResultsDistance to optimal
Aglycons
Estrogen-like Isoflavonoids
![Page 20: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/20.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
ResultsPrediction qualityAglycons
Estrogen-like Isoflavonoids
![Page 21: BEST - B YG E N S UND T ILVÆRELSE QSAR & C HEMOMETRICS Åsmund Rinnan Royal Veterinary and Agricultural University Denmark aar@kvl.dk QxPR methods in biomedicine.](https://reader035.fdocuments.net/reader035/viewer/2022070308/551c300e550346a84f8b62f2/html5/thumbnails/21.jpg)
BEST - BYG EN SUND TILVÆRELSE QSAR & CHEMOMETRICSÅsmund Rinnan
Royal Veterinary and Agricultural UniversityDenmark
Conclusion
UFF
AM1
PM3 HF
B3LYP
Mechanical Semi-empiricalDensity
FunctionalTheorem
Time consumption
Seconds Days
Theoretical level
MM3*