Jones D T, Miller R T, Thornton J M
Department of Biochemistry and Molecular Biology, University College, London.
Proteins. 1995 Nov;23(3):387-97. doi: 10.1002/prot.340230312.
Analysis of the results of the recent protein structure prediction experiment for our method shows that we achieved a high level of success. Of the 18 available prediction targets of known structure, the assessors have identified 11 chains which either entirely match a previously known fold, or which partially match a substantial region of a known fold. Of these 11 chains, we made predictions for 9, and correctly assigned the folds in 5 cases. We have also identified a further 2 chains which also partially match known folds, and both of these were correctly predicted. The success rate for our method under blind testing is therefore 7 out of 11 chains. A further 2 folds could have easily been recognized but failed due to either overzealous filtering of potential matches, or to simple human error on our part. One of the two targets for which we did not submit a prediction, prosubtilisin, would not have been recognized by our usual criteria, but even in this case, it is possible that a correct prediction could have been made by considering a combination of pairwise energy and solvation energy Z-scores. Inspection of the threading alignments for the (alpha beta)8 barrels provides clues as to how fold recognition by threading works, in that these folds are recognized by parts rather than as a whole. The prospects for developing sequence threading technology further is discussed.
对我们方法最近的蛋白质结构预测实验结果分析表明，我们取得了很高的成功率。在18个已知结构的可用预测目标中，评估者识别出11条链，它们要么完全匹配先前已知的折叠，要么部分匹配已知折叠的一个相当大的区域。在这11条链中，我们对9条进行了预测，并在5个案例中正确地指定了折叠。我们还识别出另外2条链，它们也部分匹配已知折叠，并且这两条都被正确预测。因此，我们方法在盲测下的成功率是11条链中有7条。另外2个折叠本可以很容易地被识别出来，但由于对潜在匹配过度过滤或者我们自身的简单人为错误而未能识别。我们没有提交预测的两个目标之一，即前枯草杆菌蛋白酶，按我们通常的标准是无法识别的，但即使在这种情况下，通过考虑成对能量和溶剂化能量Z分数的组合也有可能做出正确的预测。对(αβ)8桶的穿线比对检查为穿线法的折叠识别工作方式提供了线索，因为这些折叠是被部分而非整体识别的。文中还讨论了进一步发展序列穿线技术的前景。
