Difference between revisions of "Protein modelling"
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| − | Problem (문제정의) | + | ===Problem (문제정의)=== |
* Build 3D structural models of given or interested proteins | * Build 3D structural models of given or interested proteins | ||
** Initial input: amino acid sequence of the target protein | ** Initial input: amino acid sequence of the target protein | ||
** Final output: its predicted 3D structure | ** 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: [[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) | ||
| + | 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) | ||
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)
