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Using PyMOL's Align Feature to Create a Database of Ligand Binding Site Files for the Structural Analysis of Proteins.
Author(s) -
Westin Charles W,
Hanson Brett,
Craig Paul A
Publication year - 2007
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.21.5.a296-d
Subject(s) - protein data bank (rcsb pdb) , database , computer science , protein data bank , function (biology) , plug in , protein structure database , structural bioinformatics , ligand (biochemistry) , protein ligand , data mining , bioinformatics , protein structure , chemistry , programming language , sequence database , biology , biochemistry , receptor , organic chemistry , evolutionary biology , gene , stereochemistry
When analyzing a novel protein, research scientists need reliable computerized tools to expedite the process of determining the protein's function and characteristics. To improve this process of analysis we have developed a database of small molecule binding sites using a plug‐in for the molecular ing program PyMOL. The PyMOL plug‐in saves the structural arrangement of the residues that surround the ligand of interest as a PDB file. A series of these small files can be readily created and used to populate a ligand database. These small PDB files can then be systematically loaded into PyMOL with the protein of interest. The protein of interest is then compared to the ligand binding site database using the PyMOL align function, resulting in RMS values for the structural alignment. This information can be reviewed after the entire ligand database has been aligned against the protein of interest, and alignments with low RMS values can be studied to determine relevance. These new tools streamline an otherwise difficult and time consuming process, and should be a valuable tool for structural biologists. Future work on the ligand binding database will include building a server to which scientists will be able to submit their own binding site data files (created with our plug‐in) to the database. The database can then be accessed by other scientists, giving them new possibilities for avenues of study.