i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10
Open Access
- 19 July 2013
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 8 (7), e69648
- https://doi.org/10.1371/journal.pone.0069648
Abstract
Protein structure refinement refers to the process of improving the qualities of protein structures during structure modeling processes to bring them closer to their native states. Structure refinement has been drawing increasing attention in the community-wide Critical Assessment of techniques for Protein Structure prediction (CASP) experiments since its addition in 8th CASP experiment. During the 9th and recently concluded 10th CASP experiments, a consistent growth in number of refinement targets and participating groups has been witnessed. Yet, protein structure refinement still remains a largely unsolved problem with majority of participating groups in CASP refinement category failed to consistently improve the quality of structures issued for refinement. In order to alleviate this need, we developed a completely automated and computationally efficient protein 3D structure refinement method, 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. Here we provide the community with free access to i3Drefine software and systematically analyse the performance of i3Drefine in strict blind mode on the refinement targets issued in CASP10 refinement category and compare with other state-of-the-art refinement methods participating in CASP10. 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 is freely available at http://protein.rnet.missouri.edu/i3drefine/.Keywords
This publication has 31 references indexed in Scilit:
- Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation SamplingStructure, 2011
- CASP9 assessment of free modeling target predictionsProteins-Structure Function and Bioinformatics, 2011
- Assessment of protein structure refinement in CASP9Proteins-Structure Function and Bioinformatics, 2011
- The other 90% of the protein: Assessment beyond the Cαs for CASP8 template‐based and high‐accuracy modelsProteins-Structure Function and Bioinformatics, 2009
- Assessment of the protein‐structure refinement category in CASP8Proteins-Structure Function and Bioinformatics, 2009
- Protein model refinement using an optimized physics-based all-atom force fieldProceedings of the National Academy of Sciences of the United States of America, 2008
- Refining homology models by combining replica‐exchange molecular dynamics and statistical potentialsProteins-Structure Function and Bioinformatics, 2008
- Toward better refinement of comparative models: Predicting loops in inexact environmentsProteins-Structure Function and Bioinformatics, 2008
- Near-native structure refinement using in vacuo energy minimizationProceedings of the National Academy of Sciences of the United States of America, 2007
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresPeptide Science, 1983