期刊
JOURNAL OF STRUCTURAL BIOLOGY
卷 177, 期 2, 页码 520-531出版社
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jsb.2011.10.011
关键词
Flexible fitting; Rigid bodies; Clustering; Optimisation; Low-resolution maps; Cryo electron microscopy density fitting
资金
- Human Frontier Science Program [RGY0079/2009-C]
- MRC [G0600084]
- MRC [G0600084] Funding Source: UKRI
- Medical Research Council [G0600084] Funding Source: researchfish
We present RIBFIND, a method for detecting flexibility in protein structures via the clustering of secondary structural elements (SSEs) into rigid bodies. To test the usefulness of the method in refining atomic structures within cryoEM density we incorporated it into our flexible fitting protocol (Flex-EM). Our benchmark includes 13 pairs of protein structures in two conformations each, one of which is represented by a corresponding cryoEM map. Refining the structures in simulated and experimental maps at the 5-15 angstrom resolution range using rigid bodies identified by RIBFIND shows a significant improvement over using individual SSEs as rigid bodies. For the 15 A resolution simulated maps, using RIBFIND-based rigid bodies improves the initial fits by 40.64% on average, as compared to 26.52% when using individual SSEs. Furthermore, for some test cases we show that at the sub-nanometer resolution range the fits can be further improved by applying a two-stage refinement protocol (using RIBFIND-based refinement followed by an SSE-based refinement). The method is stand-alone and could serve as a general interactive tool for guiding flexible fitting into EM maps. (C) 2011 Elsevier Inc. All rights reserved.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据