i3Drefine software for protein 3D structure refinement and its assessment in CASP10.
i3Drefine software for protein 3D structure refinement and its assessment in CASP10.
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DOI：
10.1371/journal.pone.0069648
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Cheng J
中科院分区：
文献类型：
--
作者：
Bhattacharya D;Cheng J
蛋白质结构精化是指在结构建模过程中改善蛋白质结构的质量，使其更接近其天然状态的过程。自第八届CASP实验加入结构精修以来，结构精修在CASP实验中受到越来越多的关注。在第9次和最近结束的第10次CASP实验期间，改进目标和参与团体的数量持续增长。然而，蛋白质结构精修仍然是一个很大程度上未解决的问题，CASP精修类别中的大多数参与组未能持续提高精修所发布的结构的质量。为了缓解这一需求，我们开发了一种完全自动化和计算效率高的蛋白质3D结构细化方法，i3 Drefine，基于迭代和高度收敛的能量最小化算法，具有强大的全原子复合物理和基于知识的力场和氢键（HB）网络优化技术。在最近的社区范围内的盲法实验中，根据CASP 10实验的官方评估，i3 Drefine（作为“MULTICOM-CONSTRUCT”）被评为服务器部分的最佳方法。在这里，我们为社区提供了免费的i3 Drefined软件，并系统地分析了i3 Drefined在严格盲模式下对CASP 10细化类别中发布的细化目标的性能，并与其他参与CASP 10的最先进的细化方法进行了比较。我们的分析表明，i3 Drefine是唯一一个参与CASP 10的全自动服务器，在全球和本地结构质量指标方面都比初始结构表现出一致的改进。i3 Drefine的可执行版本可以在http://protein.rnet.missouri.edu/i3drefine/上免费获得。
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/.