Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318, USA.
Proteins. 2010 Jul;78(9):2041-8. doi: 10.1002/prot.22717.
In this work, we develop a method called fragment comparison and the template comparison (FTCOM) for assessing the global quality of protein structural models for targets of medium and hard difficulty (remote homology) produced by structure prediction approaches such as threading or ab initio structure prediction. FTCOM requires the C(alpha) coordinates of full length models and assesses model quality based on fragment comparison and a score derived from comparison of the model to top threading templates. On a set of 361 medium/hard targets, FTCOM was applied to and assessed for its ability to improve on the results from the SP(3), SPARKS, PROSPECTOR_3, and PRO-SP(3)-TASSER threading algorithms. The average TM-score improves by 5-10% for the first selected model by the new method over models obtained by the original selection procedure in the respective threading methods. Moreover, the number of foldable targets (TM-score >or= 0.4) increases from least 7.6% for SP(3) to 54% for SPARKS. Thus, FTCOM is a promising approach to template selection. Proteins 2010. (c) 2010 Wiley-Liss, Inc.
在这项工作中，我们开发了一种名为片段比较和模板比较（FTCOM）的方法，用于评估通过构象预测方法（如串联或从头预测）产生的中等和困难难度（远程同源）目标的蛋白质结构模型的整体质量。FTCOM 需要全长模型的 C（alpha）坐标，并基于片段比较和模型与顶级串联模板比较的得分来评估模型质量。在一组 361 个中/难目标中，应用 FTCOM 并评估其改进 SP（3）、SPARKS、PROSPECTOR_3 和 PRO-SP（3）-TASSER 串联算法结果的能力。与原始串联方法中的原始选择程序获得的模型相比，新方法中第一个选择模型的 TM 评分平均提高了 5-10%。此外，可折叠目标的数量（TM 评分≥0.4）从 SP（3）的最低 7.6%增加到 SPARKS 的 54%。因此，FTCOM 是一种很有前途的模板选择方法。蛋白质 2010.（c）2010 年 Wiley-Liss，Inc.
