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Community Detection for Decoy Selection in Template-free Protein Structure Prediction

Authors:

Amarda ShehuAuthors Info & Claims

BCB '18: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

Pages 621 - 627

https://doi.org/10.1145/3233547.3233703

Published: 15 August 2018 Publication History

Abstract

Significant efforts are devoted to resolving biologically-active structures in wet and dry laboratories. In particular, due to hardware and algorithmic innovations, computational methods can now obtain thousands of structures that populate the structure space of a protein of interest. With such advances, attention turns to organizing computed structures to extract the underlying organization of the structure space in service of highlighting biologically-active structural states. In this paper we report on the promise of leveraging community detection methods, designed originally to detect communities in social networks, to organize protein structure spaces probed in silico. We report on a principled comparison of such methods along several metrics and on proteins of diverse folds and lengths. More importantly, we present a rigorous evaluation in the context of decoy selection in template-free protein structure prediction. The presented results make the case that network-based community detection methods warrant further investigation to advance analysis of protein structure spaces for automated selection of biologically-active structures.

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Cited By

Kabir KAkhter NShehu A(2020)From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state modelsJournal of Bioinformatics and Computational Biology10.1142/S021972001940014617:06(1940014)Online publication date: 31-Jan-2020
https://doi.org/10.1142/S0219720019400146
Kabir KHassan LRajabi ZAkhter NShehu A(2019)Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure PredictionMolecules10.3390/molecules2405085424:5(854)Online publication date: 28-Feb-2019
https://doi.org/10.3390/molecules24050854

Index Terms

Community Detection for Decoy Selection in Template-free Protein Structure Prediction
1. Applied computing
  1. Life and medical sciences
    1. Bioinformatics
    2. Computational biology
      1. Molecular structural biology

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Information

Published In

cover image ACM Conferences

BCB '18: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

August 2018

727 pages

ISBN:9781450357944

DOI:10.1145/3233547

General Chairs:
Amarda Shehu
George Mason University, USA
,
Cathy Wu
University of Delaware, USA
,
Program Chairs:
Christina Boucher
University of Florida, USA
,
Jing Li
Case Western Reserve University, USA
,
Hongfang Liu
Mayo Clinic, USA
,
Mihai Pop
University of Maryland, USA

Copyright © 2018 ACM.

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SIGBio: ACM Special Interest Group on Bioinformatics

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 15 August 2018

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BCB '18

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SIGBio

BCB '18: 9th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

August 29 - September 1, 2018

DC, Washington, USA

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BCB '18 Paper Acceptance Rate 46 of 148 submissions, 31%;

Overall Acceptance Rate 254 of 885 submissions, 29%

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Cited By

Kabir KAkhter NShehu A(2020)From molecular energy landscapes to equilibrium dynamics via landscape analysis and markov state modelsJournal of Bioinformatics and Computational Biology10.1142/S021972001940014617:06(1940014)Online publication date: 31-Jan-2020
https://doi.org/10.1142/S0219720019400146
Kabir KHassan LRajabi ZAkhter NShehu A(2019)Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure PredictionMolecules10.3390/molecules2405085424:5(854)Online publication date: 28-Feb-2019
https://doi.org/10.3390/molecules24050854

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