Structure_search is a tool to quickly identify structural homologs 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 ids and chains sorted by similarities to mypdb.pdb
phenix.structure_search mypdb.pdb
- obtain a list of homologs of mypdb.pdb and all ligands found in structures of those homologs
phenix.structure_search 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 :
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.
get_pdb:Collect and superpose the top N homologous pdbs (default=10).
coot_display: Display superposed pdb files in coot. [default=(False/True) as E-value(>/<)1E-18].
- sequence_only: Perform Blast sequence search against PDB database using Phenix internal DB. This
option does not require network connection.
output.txt: file containing homologs of 'pdb_file' sorted by scores.
'sequences' are structure-based Ramachandran codes (see reference), not 1-letter code for amino acids.
pdb_ligand.txt (if get_ligand=True): file containing all ligands found in all homologs from this search.
superposed PDB files: Can be found in TEMPPDB_## subdirectory as prompted in the program output.
Lo WC, Huang PJ, Chang CH, Lyu PC. BMC Bioinformatics. 2007, 8:307