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Automated protein structure refinement using i3Drefine software and its assessment in CASP10

Authors:

Debswapna Bhattacharya,

Jianlin ChengAuthors Info & Claims

BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

Page 678

https://doi.org/10.1145/2506583.2506680

Published: 22 September 2013 Publication History

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Abstract

We present fully automated and computationally efficient protein 3D structure refinement software called i3Drefine, based on an iterative and highly convergent energy minimization algorithm with a powerful all-atom composite physics and knowledge-based force fields and hydrogen bonding (HB) network optimization technique. In the recent community-wide blind experiment, CASP10, i3Drefine (as 'MULTICOM-CONSTRUCT') was ranked as the best method in the server section as per the official assessment of CASP10 experiment. Our analysis demonstrates that i3Drefine is only fully-automated server participating in CASP10 exhibiting consistent improvement over the initial structures in both global and local structural quality metrics. Executable version of i3Drefine software is freely available at http://protein.rnet.missouri.edu/i3drefine/.

Index Terms

Automated protein structure refinement using i3Drefine software and its assessment in CASP10
1. Computing methodologies
  1. Modeling and simulation
    1. Model development and analysis

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Published In

BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

September 2013

987 pages

ISBN:9781450324342

DOI:10.1145/2506583

Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 22 September 2013

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Tutorial
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Refereed limited

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BCB'13

Sponsor:

SIGBio

BCB'13: ACM-BCB2013

September 22 - 25, 2013

Wshington DC, USA

Acceptance Rates

BCB'13 Paper Acceptance Rate 43 of 148 submissions, 29%;

Overall Acceptance Rate 254 of 885 submissions, 29%

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Index Terms

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Protein Structure Refinement by Iterative Fragment Exchange

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