Protein modelling

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)