A tool for calculating binding-site residues on proteins from PDB structures
1 Department of Computer Science, Utah State University, Logan, UT, USA
2 Department of Mathematics & Computer Science, Franklin & Marshall College, Lancaster, PA, USA
BMC Structural Biology 2009, 9:52 doi:10.1186/1472-6807-9-52Published: 3 August 2009
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 protein. Thus, this requires researchers to find all PDB complexes that contain the protein of interest and combine the binding-site information gleaned from them. This process is very time-consuming. Especially, combing binding-site information obtained from different PDB structures requires tedious work to align protein sequences. The process becomes overwhelmingly difficult when researchers have a large set of proteins to analyze, which is usually the case in practice.
In this study, we have developed a
The developed tool is very useful for the research on protein binding site analysis and prediction.