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

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 calcula...

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Autores principales: Hu, Jing, Yan, Changhui
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728722/
https://www.ncbi.nlm.nih.gov/pubmed/19650927
http://dx.doi.org/10.1186/1472-6807-9-52
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author Hu, Jing
Yan, Changhui
author_facet Hu, Jing
Yan, Changhui
author_sort Hu, Jing
collection PubMed
description 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 . 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.
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spelling pubmed-27287222009-08-19 A tool for calculating binding-site residues on proteins from PDB structures Hu, Jing Yan, Changhui BMC Struct Biol Software 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 . 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. BioMed Central 2009-08-03 /pmc/articles/PMC2728722/ /pubmed/19650927 http://dx.doi.org/10.1186/1472-6807-9-52 Text en Copyright © 2009 Hu and Yan; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Hu, Jing
Yan, Changhui
A tool for calculating binding-site residues on proteins from PDB structures
title A tool for calculating binding-site residues on proteins from PDB structures
title_full A tool for calculating binding-site residues on proteins from PDB structures
title_fullStr A tool for calculating binding-site residues on proteins from PDB structures
title_full_unstemmed A tool for calculating binding-site residues on proteins from PDB structures
title_short A tool for calculating binding-site residues on proteins from PDB structures
title_sort tool for calculating binding-site residues on proteins from pdb structures
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2728722/
https://www.ncbi.nlm.nih.gov/pubmed/19650927
http://dx.doi.org/10.1186/1472-6807-9-52
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