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A tool for calculating binding-site residues on proteins from PDB structures

Jing Hu12 and Changhui Yan1*

Author Affiliations

1 Department of Computer Science, Utah State University, Logan, UT, USA

2 Department of Mathematics & Computer Science, Franklin & Marshall College, Lancaster, PA, USA

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BMC Structural Biology 2009, 9:52  doi:10.1186/1472-6807-9-52

Published: 3 August 2009

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 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.

Results

In this study, we have developed a

    t
ool for
    c
alculating
    b
inding-site
    r
esidues on
    p
roteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit webcite. For an input protein, TCBRP can quickly find all binding-site residues on the protein by automatically combining the information obtained from all PDB structures that consist of the protein of interest. Additionally, TCBRP presents the binding-site residues in different categories according to the interaction type. TCBRP also allows researchers to set the definition of binding-site residues.

Conclusion

The developed tool is very useful for the research on protein binding site analysis and prediction.