THREADING A DATABASE OF PROTEIN CORES
THREADING A DATABASE OF PROTEIN CORES
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DOI：
10.1002/prot.340230309
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发表时间：
1995-11-01
影响因子：
2.9
通讯作者：
BRYANT, SH
中科院分区：
文献类型：
--
作者：
MADEJ, T;GIBRAT, JF;BRYANT, SH
我们提出了一个分析10盲预测准备最近的会议，“关键评估技术蛋白质结构预测。（1）这些蛋白质的序列与当时可用的结构数据库中的任何蛋白质的序列都没有可检测的相似性，但我们试图通过线程方法识别与已知结构域折叠的相似性。正如我们随后了解到的那样，这10种蛋白质中有4种确实与当时已知的结构具有显著的相似性。对于这些蛋白质中的2个，预测是准确的，在这个意义上，类似的结构位于或接近线程得分列表的顶部，并且线程对齐与相应的结构对齐一致。对于最佳预测模型，相对于最佳结构比对的平均比对误差为2.7个残基，完全由链或螺旋的小“寄存器移位”引起。在分析中，我们试图确定导致这些成功和失败的因素，由于我们的穿线方法不使用空位罚分，我们可以容易地区分由我们先前对已知结构的“核心”的定义引起的错误和由穿线潜力的固有限制引起的错误，从结果中可以看出，成功的子结构识别最关键地取决于数据库蛋白质的“折叠”的准确定义。这个定义必须正确地描述亚结构，是，不，可能是保守的蛋白质进化过程中。(C)1995年Wiley-Liss，Inc.*
We present an analysis of 10 blind predictions prepared for a recent conference, ''Critical Assessment of Techniques for Protein Structure Prediction.''(1) The sequences of these proteins are not detectably similar to those of any protein in the structure database then available, but we attempted, by a threading method, to recognize similarity to known domain folds. Four of the 10 proteins, as we subsequently learned, do indeed show significant similarity to then-known structures. For 2 of these proteins the predictions were accurate, in the sense that a similar structure was at or near the top of the list of threading scores, and the threading alignment agreed well with the corresponding structural alignment. For the best predicted model mean alignment error relative to the optimal structural alignment was 2.7 residues, arising entirely from small ''register shifts'' of strands or helices. In the analysis we attempt to identify factors responsible for these successes and failures, Since our threading method does not use gap penalties, we may readily distinguish between errors arising from our prior definition of the ''cores'' of known structures and errors arising from inherent limitations in the threading potential, It would appear from the results that successful substructure recognition depends most critically on accurate definition of the ''fold'' of a database protein. This definition must correctly delineate substructures that are, and are not, likely to be conserved during protein evolution. (C) 1995 Wiley-Liss, Inc.*