A tool for calculating binding-site residues on proteins from PDB structures |
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Authors: | Jing Hu Changhui Yan |
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Affiliation: | (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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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. |
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