20081104 Modeller Tutorial

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Marc A. Marti-Renomhttp://bioinfo.cipf.es/sgu/

Structural Genomics Unit

Bioinformatics Department

Prince Felipe Resarch Center (CIPF), Valencia, Spain

Comparative Protein Structure PredictionMODELLER tutorial
http://bioinfo.cipf.es/sgu/http://bioinfo.cipf.es/sgu/


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Obtaining MODELLER and related

information

MODELLER (9v5) web pagehttp://www.salilab.org/modeller/

Download Software (Linux/Windows/Mac/Solaris)

HTML Manual

Join Mailing List

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http://www.salilab.org/modeller/http://www.salilab.org/modeller/


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Using MODELLER

No GUI! !

Controlled by command file !!Script is written in PYTHON language "

You may know Python language is simple ""

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INPUT:

Target Sequence (FASTA/PIR format)

Template Structure (PDB format)

Python file

OUTPUT:

Target-Template Alignment

Model in PDB formatOther data

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Using MODELLER


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Modeling of BLBPInput

Target: Brain lipid-binding protein (BLBP)

BLBP sequence in PIR (MODELLER) format:

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Modeling of BLBPSTEP 1: Alignblbpand1hmssequences

Python script for target-template alignment

Run by typing mod9v5 align.py in the directory where you have the python file.MODELLER will produce a align.log file

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Modeling of BLBPSTEP 1: Align blbp and 1hms sequences

Output

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Output

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Output

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Modeling of BLBPSTEP 2: Model the blbp structure using the

alignment from step 1.

Python script for model building

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Run by typing mod9v5 model.py in the directory where you have the python file.MODELLER will produce a model.log file


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Model file#blbp.B99990001.pdb

PDB file

Can be viewed with Chimera

http://www.cgl.ucsf.edu/chimera/

Rasmol

http://www.openrasmol.org

PyMol

http://pymol.sourceforge.net/

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http://www.expasy.org/spdbv/http://www.openrasmol.org/http://www.openrasmol.org/http://www.cgl.ucsf.edu/chimera/http://www.cgl.ucsf.edu/chimera/http://www.expasy.org/spdbv/


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http://www.salilab.org/modeller/tutorial/

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http://www.salilab.org/modeller/tutorial/http://www.salilab.org/modeller/tutorial/


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MODWEBhttp://salilab.org/modweb
http://salilab.org/modwebhttp://salilab.org/modweb


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MODBASEhttp://salilab.org/modbase

Pieper et al. (2004) Nucleic Acids Research 32, D217-D222

Search PageModel Details

Model Overview

Sequence Overview


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take home message

20 D. Baker & A. Sali. Science 294, 93, 2001.

20081104 Modeller Tutorial

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