research-article

Variational Bayesian clustering on protein cavity conformations for detecting influential amino acids

Authors:

Brian Y. ChenAuthors Info & Claims

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

Pages 703 - 710

https://doi.org/10.1145/2649387.2660837

Published: 20 September 2014 Publication History

Abstract

Proteins are large flexible biological molecules and conformational flexibility is a shared challenge in comparisons of protein structure. Many tools have been developed to identify remote homologs in cases where backbone flexibilities are considered. However, these methods require comparisons of structures of more than one proteins, and this is not always available. To assist this process, this paper presents an unsupervised method to predict amino acids that exhibit substantial flexibility to change the binding site when only one protein structure is available. Our method is applied on conformational samples of sequentially nonredundant structures of the serine protease proteins. We observed that influential amino acids can be predicted with high specificities in our whole data set. The results suggest our method as a tool to detect significant side chain motions that affect binding specificity of one protein in the presence of great flexibility.

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Cited By

Stevenson GKirshner DBennion BYang YZhang XZemla ATorres MEpstein AJones DKim HBennett WWong SAllen JLightstone F(2023)Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization MethodJournal of Chemical Information and Modeling10.1021/acs.jcim.3c0072263:21(6655-6666)Online publication date: 17-Oct-2023
https://doi.org/10.1021/acs.jcim.3c00722
Li NZhou JWang HWang CMu CShi CLiu L(2020) Effect of light intensity on digestion and immune responses, plasma cortisol and amino acid composition of Scylla paramamosain during indoor overwintering Aquaculture Research10.1111/are.14836Online publication date: 26-Aug-2020
https://doi.org/10.1111/are.14836
Guo ZChen B(2016)A map of binding cavity conformations reveals differences in binding specificity2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)10.1109/BIBM.2016.7822486(13-19)Online publication date: Dec-2016
https://doi.org/10.1109/BIBM.2016.7822486
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Index Terms

Variational Bayesian clustering on protein cavity conformations for detecting influential amino acids
1. Applied computing
  1. Life and medical sciences

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cover image ACM Conferences

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

September 2014

851 pages

ISBN:9781450328944

DOI:10.1145/2649387

General Chairs:
Pierre Baldi
University of California, Irvine
,
Wei Wang
University of California, Los Angeles

Copyright © 2014 ACM.

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Published: 20 September 2014

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September 20 - 23, 2014

California, Newport Beach

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Cited By

Stevenson GKirshner DBennion BYang YZhang XZemla ATorres MEpstein AJones DKim HBennett WWong SAllen JLightstone F(2023)Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization MethodJournal of Chemical Information and Modeling10.1021/acs.jcim.3c0072263:21(6655-6666)Online publication date: 17-Oct-2023
https://doi.org/10.1021/acs.jcim.3c00722
Li NZhou JWang HWang CMu CShi CLiu L(2020) Effect of light intensity on digestion and immune responses, plasma cortisol and amino acid composition of Scylla paramamosain during indoor overwintering Aquaculture Research10.1111/are.14836Online publication date: 26-Aug-2020
https://doi.org/10.1111/are.14836
Guo ZChen B(2016)A map of binding cavity conformations reveals differences in binding specificity2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)10.1109/BIBM.2016.7822486(13-19)Online publication date: Dec-2016
https://doi.org/10.1109/BIBM.2016.7822486
Guo ZScheinberg KJuliana Hong Chen B(2015)Superposition of protein structures using electrostatic isopotentialsProceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)10.1109/BIBM.2015.7359658(75-82)Online publication date: 9-Nov-2015
https://dl.acm.org/doi/10.1109/BIBM.2015.7359658
Guo ZChen B(2015)Conformational Sampling Reveals Amino Acids with a Steric Influence on SpecificityJournal of Computational Biology10.1089/cmb.2015.011722:9(861-875)Online publication date: Sep-2015
https://doi.org/10.1089/cmb.2015.0117

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