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===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: [[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)
