Assessment of ligand-binding residue predictions in CASP9.
Assessment of ligand-binding residue predictions in CASP9.
复制标题
作者：
Schmidt T;Haas J;Gallo Cassarino T;Schwede T
蛋白质与其配体之间的相互作用在许多生理过程中起着核心作用。然而，这些相互作用中的大多数结构细节还没有被经验地描述出来。因此，人们开发了各种计算工具来预测与配体相互作用的结合部位和氨基酸残基的位置。在这篇手稿中，我们评估了参与CASP9中配体结合位点预测类别的33种方法的性能。CASP9中配体结合位点预测的总体准确性似乎相当高(表现最好的十个组的平均MCC为0.62)，与之前的实验相比，更多的组表现得同样好。然而，这应该在测试数据强烈偏向于基于简单模板的模型的背景下看到。总体而言，表现最好的方法已经收敛到使用来自相关同源结构的配体结合位点推断的类似方法，这限制了它们对困难的“从头”预测目标的适用性。在这里，我们介绍了CASP9对配体结合位点类别的评估结果，讨论了CASP9中成功和具有挑战性的预测目标的例子，最后建议改变实验的形式，以克服目前评估的局限性。
Interactions between proteins and their ligands play central roles in many physiological processes. The structural details for most of these interactions, however, have not yet been characterized experientially. Therefore, various computational tools have been developed to predict the location of binding sites and the amino acid residues interacting with ligands. In this manuscript, we assess the performance of 33 methods participating in the ligand binding site prediction category in CASP9. The overall accuracy of ligand binding site predictions in CASP9 appears rather high (average MCC of 0.62 for the ten top performing groups), and compared to previous experiments more groups performed equally well. However, this should be seen in context of a strong bias in the test data towards easy template based models. Overall, the top performing methods have converged to a similar approach using ligand binding site inference from related homologous structures, which limits their applicability for difficult “de novo” prediction targets. Here, we present the results of the CASP9 assessment of the ligand binding site category, discuss examples for successful and challenging prediction targets in CASP9, and finally suggest changes in the format of the experiment to overcome the current limitations of the assessment.
登录
查看更多内容
影响因子：
--
作者：
Huang B;Schroeder M
通讯作者：
Schroeder M
影响因子：
2.9
作者：
Lopez, Gonzalo;Rojas, Ana;Valencia, Alfonso
通讯作者：
Valencia, Alfonso
影响因子：
5.8
作者：
Pazos, Florencio;Rausell, Antonio;Valencia, Alfonso
通讯作者：
Valencia, Alfonso
DOI：
10.1016/0005-2795(75)90109-9
发表时间：
1975-01-01
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA
影响因子：
--
作者：
MATTHEWS, BW
通讯作者：
MATTHEWS, BW
影响因子：
14.9
作者：
Lopez, Gonzalo;Valencia, Alfonso;Tress, Michael L.
通讯作者：
Tress, Michael L.