Difference between revisions of "Protein modelling"
| Line 8: | Line 8: | ||
===Method=== | ===Method=== | ||
| − | Find one or more structural templates of the target protein via sequence homology search against known structures (program: BLASTP or PSI-BLAST, database: PDB) | + | * Find one or more structural templates of the target protein via sequence homology search against known structures (program: BLASTP or PSI-BLAST, database: PDB) |
| − | Download template structures in PDB format (web server: RCSB PDB) | + | |
| − | Align the amino acid sequence of the target protein with that(those) of the template protein(s) (program: CLUSTALW, output: PIR format) | + | * Download template structures in PDB format (web server: RCSB PDB) |
| − | Build 3D structural models based on the multiple sequence alignment and the template 3D structure(s) (program: MODELLER, input: ATM, ALI, and TOP files) | + | * Align the amino acid sequence of the target protein with that(those) of the template protein(s) (program: CLUSTALW, output: PIR format) |
| + | * Build 3D structural models based on the multiple sequence alignment and the template 3D structure(s) (program: MODELLER, input: ATM, ALI, and TOP files) | ||
manual build | manual build | ||
manually convert file formats from PDB to ATM and PIR to ALI, respectively | manually convert file formats from PDB to ATM and PIR to ALI, respectively | ||
| Line 18: | Line 19: | ||
automatic build (some PDB and PIR files are not successfully converted to correct ATM and ALI files due to amino-acid sequence mismatch) | automatic build (some PDB and PIR files are not successfully converted to correct ATM and ALI files due to amino-acid sequence mismatch) | ||
perl script to generate ATM, ALI, and TOP files from PDB and PIR files: [[perl script for ATM|txt]], gz | perl script to generate ATM, ALI, and TOP files from PDB and PIR files: [[perl script for ATM|txt]], gz | ||
| + | |||
command-line arguments in order: base_directory_path pir_file_name target_protein_id(exactly 4 letters) one_or_more_PDB_file_names(exactly 4-letter prefix) | command-line arguments in order: base_directory_path pir_file_name target_protein_id(exactly 4 letters) one_or_more_PDB_file_names(exactly 4-letter prefix) | ||
run the perl script (e.g. ../bin/makeModellerInput.pl /home/user/Protein3DModelling/KCIP KCIP.pir KCIP 1QJA.pdb) | run the perl script (e.g. ../bin/makeModellerInput.pl /home/user/Protein3DModelling/KCIP KCIP.pir KCIP 1QJA.pdb) | ||
Revision as of 09:33, 26 August 2005
http://biome.ngic.re.kr/ProteinModelling/
Problem (문제정의)
- Build 3D structural models of given or interested proteins
- Initial input: amino acid sequence of the target protein
- Final output: its predicted 3D structure
Method
- Find one or more structural templates of the target protein via sequence homology search against known structures (program: BLASTP or PSI-BLAST, database: PDB)
- Download template structures in PDB format (web server: RCSB PDB)
- Align the amino acid sequence of the target protein with that(those) of the template protein(s) (program: CLUSTALW, output: PIR format)
- Build 3D structural models based on the multiple sequence alignment and the template 3D structure(s) (program: MODELLER, input: ATM, ALI, and TOP files)
manual build manually convert file formats from PDB to ATM and PIR to ALI, respectively write a TOP script file run MODELLER automatic build (some PDB and PIR files are not successfully converted to correct ATM and ALI files due to amino-acid sequence mismatch) perl script to generate ATM, ALI, and TOP files from PDB and PIR files: txt, gz
command-line arguments in order: base_directory_path pir_file_name target_protein_id(exactly 4 letters) one_or_more_PDB_file_names(exactly 4-letter prefix) run the perl script (e.g. ../bin/makeModellerInput.pl /home/user/Protein3DModelling/KCIP KCIP.pir KCIP 1QJA.pdb) run MODELLER (e.g. mod7v7 KCIP.top) example ATM file: 5fd1.atm ALI file: alignment.ali TOP file: model-default.top command: mod7v7 model-default.top output PDB file (predicted model): 1fdx.B99990001.pdb MODELLER manual PDF, HTML Display and compare the 3D structures of the model and the template proteins (program: RasMol)
