title: A tool for calculating binding-site residues on proteins from PDB structures.
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 tool for calculating binding-site residues on proteins, TCBRP http://yanbioinformatics.cs.usu.edu:8080/ppbindingsubmit. 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.
  
  
  CONCLUSIONS
  The developed tool is very useful for the research on protein binding site analysis and prediction.
authors: Department of Computer Science, Utah State University, Logan, UT, USA. jing.hu@fandm.edu
authors: Jing
authors: J
authors: Hu
authors: Changhui
authors: C
authors: Yan
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry; D030562:Databases, Protein; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012984:Software; D014764:Viral Proteins / Q000737:chemistry
chemical_list: D014764:Viral Proteins; C062210:bacteriophage T7 RNA polymerase; D012321:DNA-Directed RNA Polymerases