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From Opengenome.net
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* 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)
