Comparative Protein Structure Prediction MODELLER tutorial
$>mod9v5 [Link]
Marc A. Marti-Renom
[Link]
Structural Genomics Unit Bioinformatics Department Prince Felipe Resarch Center (CIPF), Valencia, Spain
Obtaining MODELLER and related information
MODELLER (9v5) web page
[Link] Download Software (Linux/Windows/Mac/Solaris) HTML Manual Join Mailing List
Using MODELLER
No GUI! ! Controlled by command file !! Script is written in PYTHON language " You may know Python language is simple ""
Using MODELLER
INPUT: Target Sequence (FASTA/PIR format) Template Structure (PDB format) Python file OUTPUT: Target-Template Alignment Model in PDB format Other data
Modeling of BLBP Input
Target: Brain lipid-binding protein (BLBP) BLBP sequence in PIR (MODELLER) format:
>P1;blbp sequence:blbp:::::::: VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGGKVVIRTQCTFKNTEINFQLGEEFEETSIDDRNCKSVV RLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFGDIVAVRCYEKA*
Modeling of BLBP STEP 1: Align blbp and 1hms sequences Python script for target-template alignment
# Example for: [Link]() # This will read two sequences, align them, and write the alignment # to a file: [Link]() env = environ() aln = alignment(env) mdl = model(env, file='1hms') aln.append_model(mdl, align_codes='1hms') [Link](file='[Link]', align_codes=('blbp')) # The [Link] similarity matrix is used by default: [Link](gap_penalties_1d=(-600, -400)) [Link](file='[Link]', alignment_format='PIR') [Link](file='[Link]', alignment_format='PAP')
Run by typing mod9v5 [Link] in the directory where you have the python file. MODELLER will produce a [Link] file
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Modeling of BLBP STEP 1: Align blbp and 1hms sequences Python script for target-template alignment
# Example for: [Link]() # This will read two sequences, align them, and write the alignment # to a file: [Link]() env = environ() aln = alignment(env) mdl = model(env, file='1hms') aln.append_model(mdl, align_codes='1hms') [Link](file='[Link]', align_codes=('blbp')) # The [Link] similarity matrix is used by default: [Link](gap_penalties_1d=(-600, -400)) [Link](file='[Link]', alignment_format='PIR') [Link](file='[Link]', alignment_format='PAP')
Run by typing mod9v5 [Link] in the directory where you have the python file. MODELLER will produce a [Link] file
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Modeling of BLBP STEP 1: Align blbp and 1hms sequences Python script for target-template alignment
# Example for: [Link]() # This will read two sequences, align them, and write the alignment # to a file: [Link]() env = environ() aln = alignment(env) mdl = model(env, file='1hms') aln.append_model(mdl, align_codes='1hms') [Link](file='[Link]', align_codes=('blbp')) # The [Link] similarity matrix is used by default: [Link](gap_penalties_1d=(-600, -400)) [Link](file='[Link]', alignment_format='PIR') [Link](file='[Link]', alignment_format='PAP')
Run by typing mod9v5 [Link] in the directory where you have the python file. MODELLER will produce a [Link] file
8
Modeling of BLBP STEP 1: Align blbp and 1hms sequences Python script for target-template alignment
# Example for: [Link]() # This will read two sequences, align them, and write the alignment # to a file: [Link]() env = environ() aln = alignment(env) mdl = model(env, file='1hms') aln.append_model(mdl, align_codes='1hms') [Link](file='[Link]', align_codes=('blbp')) # The [Link] similarity matrix is used by default: [Link](gap_penalties_1d=(-600, -400)) [Link](file='[Link]', alignment_format='PIR') [Link](file='[Link]', alignment_format='PAP')
Run by typing mod9v5 [Link] in the directory where you have the python file. MODELLER will produce a [Link] file
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Modeling of BLBP STEP 1: Align blbp and 1hms sequences Output
>P1;1hms structureX:1hms: 1 : : 131 : :undefined:undefined:-1.00:-1.00 VDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNTEISFKLGVEFDETTA DDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHGTAVCTRTYEKE* >P1;blbp sequence:blbp: : : : : : : 0.00: 0.00 VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGGKVVIRTQCTFKNTEINFQLGEEFEETSI DDRNCKSVVRLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFGDIVAVRCYEKA*
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Modeling of BLBP STEP 1: Align blbp and 1hms sequences Output
>P1;1hms structureX:1hms: 1 : : 131 : :undefined:undefined:-1.00:-1.00 VDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNTEISFKLGVEFDETTA DDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHGTAVCTRTYEKE* >P1;blbp sequence:blbp: : : : : : : 0.00: 0.00 VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGGKVVIRTQCTFKNTEINFQLGEEFEETSI DDRNCKSVVRLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFGDIVAVRCYEKA*
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Modeling of BLBP STEP 1: Align blbp and 1hms sequences Output
_aln.pos 10 20 30 40 50 60 1hms VDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNTEISFKLGV blbp VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGGKVVIRTQCTFKNTEINFQLGE _consrvd **** **** ** *** *** ********** **** ** * * ******* * ** _aln.p 1hms blbp _consrvd 70 80 90 100 110 120 130 EFDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHGTAVCTRTYEKE EFEETSIDDRNCKSVVRLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFGDIVAVRCYEKA ** ** *** ** * *** ** * ***** ** ** *** *** * * * ***
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Modeling of BLBP STEP 2: Model the blbp structure using the alignment from step 1. Python script for model building
# Homology modelling by the automodel class from [Link] import * # Load the automodel class [Link]() !! ! ! ! ! # request verbose output env = environ() ! ! ! ! ! ! # create a new MODELLER environment ! ! ! ! ! ! ! ! ! ! # directories for input atom files [Link].atom_files_directory = './:../atom_files' a = automodel(env, alnfile = '[Link]', # alignment filename knowns = '1hms', # codes of the templates sequence = 'blbp') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) [Link]() # do the actual homology modelling
Run by typing mod9v5 [Link] in the directory where you have the python file. MODELLER will produce a [Link] file
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Modeling of BLBP STEP 2: Model the blbp structure using the alignment from step 1. Python script for model building
# Homology modelling by the automodel class from [Link] import * # Load the automodel class [Link]() !! ! ! ! ! # request verbose output env = environ() ! ! ! ! ! ! # create a new MODELLER environment ! ! ! ! ! ! ! ! ! ! # directories for input atom files [Link].atom_files_directory = './:../atom_files' a = automodel(env, alnfile = '[Link]', # alignment filename knowns = '1hms', # codes of the templates sequence = 'blbp') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) [Link]() # do the actual homology modelling
Run by typing mod9v5 [Link] in the directory where you have the python file. MODELLER will produce a [Link] file
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Modeling of BLBP STEP 2: Model the blbp structure using the alignment from step 1. Python script for model building
# Homology modelling by the automodel class from [Link] import * # Load the automodel class [Link]() !! ! ! ! ! # request verbose output env = environ() ! ! ! ! ! ! # create a new MODELLER environment ! ! ! ! ! ! ! ! ! ! # directories for input atom files [Link].atom_files_directory = './:../atom_files' a = automodel(env, alnfile = '[Link]', # alignment filename knowns = '1hms', # codes of the templates sequence = 'blbp') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) [Link]() # do the actual homology modelling
Run by typing mod9v5 [Link] in the directory where you have the python file. MODELLER will produce a [Link] file
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Modeling of BLBP STEP 2: Model the blbp structure using the alignment from step 1. Python script for model building
PDB file Can be viewed with Chimera
[Link]
Rasmol
[Link]
PyMol
[Link]
Model file # [Link]
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[Link]
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MODWEB
[Link]
MODBASE
[Link]
Search Page Model Details
Sequence Overview
Model Overview
Pieper et al. (2004) Nucleic Acids Research 32, D217-D222
take home message
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D. Baker & A. Sali. Science 294, 93, 2001.
