a tool for calculating binding-site residues on proteins from pdb structures计算工具结合位点从pdb残留在蛋白质结构.pdfVIP

BMC Structural Biology BioMed Central Software Open Access A tool for calculating binding-site residues on proteins from PDB structures Jing Hu1,2 and Changhui Yan*1 Address: 1Department of Computer Science, Utah State University, Logan, UT, USA and 2Department of Mathematics Computer Science, Franklin Marshall College, Lancaster, PA, USA Email: Jing Hu - jing.hu@; Changhui Yan* - charles.yan@ * Corresponding author Published: 3 August 2009 Received: 1 March 2009 Accepted: 3 August 2009 BMC Structural Biology 2009, 9:52 doi:10.1186/1472-6807-9-52 This article is available from: /1472-6807/9/52 © 2009 Hu and Yan; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: In the research on protein functional sites, researchers often need to identify binding-site residues on a protein. A commonly used strategy is to find a complex structure from the Protein Data Bank (PDB) that consists of the protein of interest and its interacting partner(s) and calculate binding-site residues based on the complex structure. However, since a protein may participate in multiple interactions, the binding-site residues calculated based on one complex structure usually do not reveal all binding sites on a pro