Ab initio protein structure prediction using Chunk-TASSER
Ab initio protein structure prediction using Chunk-TASSER
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DOI：
10.1529/biophysj.107.109959
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发表时间：
2007-09-01
影响因子：
3.4
通讯作者：
Skolnick, Jeffrey
中科院分区：
文献类型：
--
作者：
Zhou, Hongyi;Skolnick, Jeffrey
我们开发了一种名为Chunk-Tasser的从头算蛋白质结构预测方法，该方法使用给定靶标的从头计算折叠超二级结构块以及穿线模板来获得接触势和距离约束。根据新的片段比较方法选择的预测块通过片段插入方法折叠。全长模型由Tasser方法建立和改进，该方法通过并行双曲蒙特卡罗搜索构象空间。我们采用了优化的简化力场，该力场包括基于知识的统计势和来自组块的约束以及线程模板。该方法在425个硬靶蛋白=50%的数据集上进行了测试，这些平均值分别为0.284、0.356和0.403。通过SP3、Tasser和Chunk-Tasser，前五个模型中最好的具有TM-Score>；=0.4(结构相似性的统计显著阈值)的蛋白质的百分比总体上分别为3.76、20.94和28.94%，而对于80个主要螺旋蛋白质的子集，这些百分比分别为2.50、23.75和41.25%。因此，在无法识别好的模板的情况下，组块Tasser在建模硬目标方面显示出比Tasser显著的改进。我们还在21个中/硬目标上进行了组块测试，其中200个氨基酸来自CASP7。在第一个(前五名中最好的)模型的总TM得分方面，Chunk-Tasser与Tasser相似(10%)。Chunk-Tasser是全自动的，可用于蛋白质组尺度的蛋白质结构预测。
We have developed an ab initio protein structure prediction method called chunk-TASSER that uses ab initio folded supersecondary structure chunks of a given target as well as threading templates for obtaining contact potentials and distance restraints. The predicted chunks, selected on the basis of a new fragment comparison method, are folded by a fragment insertion method. Full-length models are built and refined by the TASSER methodology, which searches conformational space via parallel hyperbolic Monte Carlo. We employ an optimized reduced force field that includes knowledge-based statistical potentials and restraints derived from the chunks as well as threading templates. The method is tested on a dataset of 425 hard target proteins = 50%, these averages are 0.284, 0.356, and 0.403, respectively. The percentages of proteins with the best of top five models having TM-score >= 0.4 ( a statistically significant threshold for structural similarity) are 3.76, 20.94, and 28.94% by SP3, TASSER, and chunk-TASSER, respectively, overall, while for the subset of 80 predominantly helical proteins, these percentages are 2.50, 23.75, and 41.25%. Thus, chunk-TASSER shows a significant improvement over TASSER for modeling hard targets where no good template can be identified. We also tested chunk-TASSER on 21 medium/hard targets, 200 amino-acids-long from CASP7. Chunk-TASSER is similar to 11% (10%) better than TASSER for the total TM-score of the first ( best of top five) models. Chunk-TASSER is fully automated and can be used in proteome scale protein structure prediction.