CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data.
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data.
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DOI：
10.1093/nar/gkn305
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发表时间：
2008-07-01
影响因子：
14.9
通讯作者：
Lin G
中科院分区：
文献类型：
--
作者：
Wishart DS;Arndt D;Berjanskii M;Tang P;Zhou J;Lin G
CS23 D（化学位移到3D结构）是一个Web服务器，用于仅使用指定的核磁共振（NMR）化学位移和序列数据作为输入快速生成准确的3D蛋白质结构。与传统的NMR方法不同，CS23 D不需要NOE和/或J-耦合数据来执行其计算。CS23 D接受SHIFTY或BMRB格式的化学位移文件，并在大约10-15分钟内生成一组蛋白质的PDB坐标。CS23 D使用多个预先存在的程序或服务器的管道来计算实际的蛋白质结构。根据序列相似性（或缺乏序列相似性），CS23 D使用（i）最大亚片段组装（同源性建模的一种形式），（ii）化学位移线程或（iii）位移辅助从头结构预测（通过Rosetta），然后进行化学位移细化，以生成和/或细化蛋白质坐标。对来自BioMagResBank的100多种蛋白质进行的测试表明，CS23 D对>95%的蛋白质查询收敛（即找到解决方案）。发现这些化学位移产生的结构与使用常规NOE-基NMR方法或常规X-射线方法产生的NMR结构在0.2-2.8 μ RMSD内。CS23 D的性能取决于化学位移分配的完整性和查询蛋白与已知3D折叠的相似性。CS23 D可在http://www.cs23d.ca上访问。
CS23D (chemical shift to 3D structure) is a web server for rapidly generating accurate 3D protein structures using only assigned nuclear magnetic resonance (NMR) chemical shifts and sequence data as input. Unlike conventional NMR methods, CS23D requires no NOE and/or J-coupling data to perform its calculations. CS23D accepts chemical shift files in either SHIFTY or BMRB formats, and produces a set of PDB coordinates for the protein in about 10–15 min. CS23D uses a pipeline of several preexisting programs or servers to calculate the actual protein structure. Depending on the sequence similarity (or lack thereof) CS23D uses either (i) maximal subfragment assembly (a form of homology modeling), (ii) chemical shift threading or (iii) shift-aided de novo structure prediction (via Rosetta) followed by chemical shift refinement to generate and/or refine protein coordinates. Tests conducted on more than 100 proteins from the BioMagResBank indicate that CS23D converges (i.e. finds a solution) for >95% of protein queries. These chemical shift generated structures were found to be within 0.2–2.8 Å RMSD of the NMR structure generated using conventional NOE-base NMR methods or conventional X-ray methods. The performance of CS23D is dependent on the completeness of the chemical shift assignments and the similarity of the query protein to known 3D folds. CS23D is accessible at http://www.cs23d.ca.