Structure_search is a tool to quickly identify structural homologues of the input PDB file from the Protein Data Bank. It uses the SARST algorithm, and it's very fast. A typical search time against the whole PDB is usually less than one second. There is an option to allow users to obtain a list of ligands found in structures of those homologs.
- obtain a list of PDB is and chains sorted by similarities to mypdb.pdb
phenix.structure_search pdb_file=mypdb.pdb
- same as above, but specify location of blast executable
phenix.structure_search pdb_file=mypdb.pdb blastpath=/my/blast/blastall
- obtain a list of homologs of mypdb.pdb and all ligands found in structures of those homologs
phenix.structure_search pdb_file=mypdb.pdb get_ligand=True
More information can be found in input/Output files sections below:
required input:
- pdb_file: the file containing the protein model of interest.
Optional inputs :
- blastpath: path to local blastall or blastall.exe (Windows) file.
- get_ligand:"=True" if want a list of ligands found in homologous PDBs, Default = False.
- job_title: Current job title
- output_prefix: prefix for output files if needed.
Lo WC, Huang PJ, Chang CH, Lyu PC. BMC Bioinformatics. 2007, 8:307