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蛋白质-蛋白质对接基准测试版本 4.0.

Protein-protein docking benchmark version 4.0.

机构信息

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

出版信息

Proteins. 2010 Nov 15;78(15):3111-4. doi: 10.1002/prot.22830.

Abstract

We updated our protein-protein docking benchmark to include complexes that became available since our previous release. As before, we only considered high-resolution complex structures that are nonredundant at the family-family pair level, for which the X-ray or NMR unbound structures of the constituent proteins are also available. Benchmark 4.0 adds 52 new complexes to the 124 cases of Benchmark 3.0, representing an increase of 42%. Thus, benchmark 4.0 provides 176 unbound-unbound cases that can be used for protein-protein docking method development and assessment. Seventeen of the newly added cases are enzyme-inhibitor complexes, and we found no new antigen-antibody complexes. Classifying the new cases according to expected difficulty for protein-protein docking algorithms gives 33 rigid body cases, 11 cases of medium difficulty, and 8 cases that are difficult. Benchmark 4.0 listings and processed structure files are publicly accessible at http://zlab.umassmed.edu/benchmark/.

摘要

我们更新了蛋白质-蛋白质对接基准测试,纳入了自上次发布以来可用的复合物。与之前一样,我们仅考虑在家族-家族对水平上是非冗余的高分辨率复合物结构,对于这些结构,其组成蛋白的 X 射线或 NMR 未结合结构也可用。基准测试 4.0 在基准测试 3.0 的 124 个案例中增加了 52 个新复合物,增加了 42%。因此,基准测试 4.0 提供了 176 个可用于蛋白质-蛋白质对接方法开发和评估的未结合-未结合案例。新添加的案例中有 17 个是酶抑制剂复合物,并且我们没有发现新的抗原-抗体复合物。根据蛋白质-蛋白质对接算法的预期难度对新案例进行分类,得到 33 个刚体案例、11 个中等难度案例和 8 个困难案例。基准测试 4.0 清单和处理后的结构文件可在 http://zlab.umassmed.edu/benchmark/ 上公开访问。

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本文引用的文献

1
The HADDOCK web server for data-driven biomolecular docking.
Nat Protoc. 2010 May;5(5):883-97. doi: 10.1038/nprot.2010.32. Epub 2010 Apr 15.
3
Accounting for conformational changes during protein-protein docking.
Curr Opin Struct Biol. 2010 Apr;20(2):180-6. doi: 10.1016/j.sbi.2010.02.001. Epub 2010 Mar 1.
4
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions.
Bioinformatics. 2008 Sep 1;24(17):1865-73. doi: 10.1093/bioinformatics/btn334. Epub 2008 Jun 30.
5
Protein-protein docking benchmark version 3.0.
Proteins. 2008 Nov 15;73(3):705-9. doi: 10.1002/prot.22106.
6
The RosettaDock server for local protein-protein docking.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W233-8. doi: 10.1093/nar/gkn216. Epub 2008 Apr 28.
8
Structure, function, and evolution of transient and obligate protein-protein interactions.
Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10930-5. doi: 10.1073/pnas.0502667102. Epub 2005 Jul 25.
9
Protein-Protein Docking Benchmark 2.0: an update.
Proteins. 2005 Aug 1;60(2):214-6. doi: 10.1002/prot.20560.
10
ClusPro: an automated docking and discrimination method for the prediction of protein complexes.
Bioinformatics. 2004 Jan 1;20(1):45-50. doi: 10.1093/bioinformatics/btg371.

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