lab 4.3 comparative modeling by m odeller roberto sanchez mount sinai school of medicine new york,...
TRANSCRIPT
Lab 4.3
Comparative Modeling
by MODELLER
Roberto Sanchez
Mount Sinai School of Medicine
New York, NY, USA
http://physbio.mssm.edu/~sanchez/
Comparative Modeling by MODELLER
• Using MODELLER
• Example 1: Modeling of BLBP
• Example 2: Protein/ligand complex model
• Example 3: Multiple template modeling
Comparative Modeling by MODELLER
• Obtaining MODELLER and related info• Using MODELLER
• Example 1: Modeling of BLBP
• Example 2: Protein/ligand complex model
• Example 3: Multiple template modeling
Obtaining MODELLER and related information
• MODELLER web pagehttp://guitar.rockefeller.edu/modeller/modeller.html
• Download Software (UNIX/Linux)
• HTML Manual
• Join Mailing List
Using MODELLER
• No GUI! • Controlled by command file (script) • Script is written in TOP language • TOP language is simple
Using MODELLER
• INPUT:• Target Sequence (PIR format)
• Template Structure (PDB format)
• TOP command file
• OUTPUT:• Target-Template Alignment
• Model in PDB format
• Other data
EXAMPLES
• Example files are in:
/PATH/examples/• Copy example files to your home directory with
the following command:
cp –R /PATH/examples .
Example 1: Modeling of BLBPINPUT
• Target: Brain lipid-binding protein (BLBP)• BLBP sequence in PIR (MODELLER) format,
file examples/ex1/blbp.seq :
>P1;blbp
sequence:blbp::::::::
VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGGKVVIRTQCTFKNTEINFQLGEEFEETSIDDRNCKSVVRLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFGDIVAVRCYEKA*
• Template search already done for you:Template: PDB file 1HMSexamples/ex1/1hms.pdb
Example 1: Modeling of BLBPSTEP 1: Align blbp and 1hms sequences TOP script for target-template alignment
File examples/ex1/align.topREAD_MODEL FILE = '1hms.pdb'
SEQUENCE_TO_ALI ALIGN_CODES = '1hms'
READ_ALIGNMENT FILE = 'blbp.seq', ALIGN_CODES = 'blbp', ADD_SEQUENCE = on
ALIGN
WRITE_ALIGNMENT FILE='blbp-1hms.ali', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE='blbp-1hms.pap', ALIGNMENT_FORMAT = 'PAP'
Run by typing mod align.top in the examples/ex1/ directory.If something goes wrong check file align.log
Example 1: Modeling of BLBPSTEP 1: Align blbp and 1hms sequences
OUTPUT
File examples/ex1/blbp-1hms.ali>P1;1hms
structureX:1hms: 1 : : 131 : :undefined:undefined:-1.00:-1.00
VDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNTEISFKLGVEFDETTA
DDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHGTAVCTRTYEKE*
>P1;blbp
sequence:blbp: : : : : : : 0.00: 0.00
VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGGKVVIRTQCTFKNTEINFQLGEEFEETSI
DDRNCKSVVRLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFGDIVAVRCYEKA*
Example 1: Modeling of BLBPSTEP 1: Align blbp and 1hms sequences
OUTPUT
File examples/ex1/blbp-1hms.pap _aln.pos 10 20 30 40 50 60
1hms VDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNT
blbp VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGGKVVIRTQCTFKNT
_consrvd **** **** ** *** *** ********** **** ** * * *****
_aln.pos 70 80 90 100 110 120
1hms EISFKLGVEFDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHG
blbp EINFQLGEEFEETSIDDRNCKSVVRLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFG
_consrvd ** * ** ** ** *** ** * *** ** * ***** ** ** *** *** *
_aln.pos 130
1hms TAVCTRTYEKE
blbp DIVAVRCYEKA
_consrvd * * ***
Example 1: Modeling of BLBPSTEP 2: Model the blbp structure using the
alignment from step 1. TOP script for model building
File examples/ex1/model.topINCLUDE
SET ALNFILE = 'blbp-1hms.ali'
SET KNOWNS = '1hms'
SET SEQUENCE = 'blbp'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1
CALL ROUTINE = 'model'
Run by typing mod model.top in the examples/ex1/ directory.If something goes wrong (or just for fun) check file model.log
Example 1: Modeling of BLBPSTEP 2: Model the blbp structure using the
alignment from step 1. OUTPUT
File examples/ex1/blbp.B99990001
• PDB file
• Can be viewed with Rasmol, PDBviewer, etc.
• Transfer from SGI server to NT workstation using ftp:
ftp server
cd examples/ex1/
get blbp.B99990001
Example 2: Modeling of a BLBP/Oleic Acid complex
INPUT
• BLBP – 1hms alignment from Example 1cd examples/ex2cp ../ex1/blbp-1hms.ali blbp-1hms-ola.ali
>P1;1hmsstructureX:1hms: 1 : : 133 : :undefined:undefined:-1.00:-1.00VDAFLGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDILTLKTHSTFKNTEISFKLGVEFDETTADDRKVKSIVTLDGGKLVHLQKWDGQETTLVRELIDGKLILTLTHGTAVCTRTYEKE.*>P1;blbpsequence:blbp: : : : : : : 0.00: 0.00VDAFCATWKLTDSQNFDEYMKALGVGFATRQVGNVTKPTVIISQEGGKVVIRTQCTFKNTEINFQLGEEFEETSIDDRNCKSVVRLDGDKLIHVQKWDGKETNCTREIKDGKMVVTLTFGDIVAVRCYEKA.*
Oleic acid molecule in 1hms PDB file is residue number 133. This can be checked by RASMOL or by looking at the PDB file directly.
Example 2: Modeling of a BLBP/Oleic Acid complex
TOP script for modeling
File examples/ex2/model2.top
Run by typing mod model2.top in the examples/ex2/ directory.If something goes wrong check file model2.log
INCLUDESET ALNFILE = 'blbp-1hms-ola.ali'SET KNOWNS = '1hms'SET SEQUENCE = 'blbp'SET STARTING_MODEL = 1SET ENDING_MODEL = 1SET HETATM_IO = onCALL ROUTINE = 'model'
Example 2: Modeling of a BLBP/Oleic Acid complex.
OUTPUT
File examples/ex2/blbp.B99990001
• View ligand with rasmol:
Menu:
Display -> backbone
Colours -> structure
Command line:
RasMol> select ligand
RasMol> color green
RasMol> cpk
Example 3: Multiple template modeling INPUT
• Target: Brain lipid-binding protein (BLBP)
• BLBP sequence in PIR (MODELLER) format,file examples/ex3/blbp.seq :
• Templates: PDB files 1HMS andexamples/ex3/1hms.pdbexamples/ex3/1lid.pdb
Example 3: Multiple template modelingSTEP 1: Align blbp and template sequences
TOP script for target-template alignment
File examples/ex3/align.topSET ALIGN_CODES = '1hms' '1lid'
SET ATOM_FILES = '1hms.pdb' '1lid.pdb'
MALIGN3D
SET ADD_SEQUENCE = on, ALIGN_BLOCK = 2
READ_ALIGNMENT FILE = 'blbp.seq', ALIGN_CODES = 'blbp'
ALIGN
WRITE_ALIGNMENT FILE = 'blbp-1hms-1lid.ali'
WRITE_ALIGNMENT FILE = 'blbp-1hms-1lid.pap', ALIGNMENT_FORMAT = 'PAP'
Run by typing mod align.top in the examples/ex3/ directory.If something goes wrong check file align.log
Example 3: Multiple template modelingSTEP 2: Model the blbp structure using the
alignment from step 1. TOP script for model building
File examples/ex3/model3.topINCLUDE
SET ALNFILE = 'blbp-1hms-1lid.ali'
SET KNOWNS = '1hms' '1lid'
SET SEQUENCE = 'blbp'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1
CALL ROUTINE = 'model'
Run by typing mod model3.top in the examples/ex3/ directory.If something goes wrong check file model3.log
Model your own protein
• Template Search (BLAST)http://www.ncbi.nlm.nih.gov/blast/
• Model Evaluation (VERIFY3D)http://www.doe-mbi.ucla.edu/verify3d.html