Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives.
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives.
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DOI：
10.1186/1471-2105-7-503
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发表时间：
2006-11-16
影响因子：
3
通讯作者：
Alexov EG
中科院分区：
文献类型：
--
作者：
Kundrotas PJ;Alexov EG
单独使用一级氨基酸序列预测残基的接触是一项重要的任务，可以指导 3D 结构建模并验证预测的 3D 结构的质量。相关突变 (CM) 方法是最有前途的方法，它已用于预测一级序列中距离较远但在同源蛋白质的天然 3D 结构中形成接触的氨基酸对。在这里，我们报告了 CM 方法的新实现，其中添加了一组选择规则（过滤器）。该算法的参数针对十五种高分辨率晶体结构进行了优化，优化标准最大限度地提高了预测的机密性。优化后，不带过滤器的 CM 的真阳性比 (TPR) 为 0.08，带过滤器的 CM 的 TPR 为 0.14。该协议进一步针对未包含在优化测试中的 65 个高分辨率结构进行了基准测试。基准测试得出，不带过滤器的 CM 的 TPR 为 0.07，带过滤器的 CM 的 TPR 为 0.09。因此，加入选择规则后，整体性能提高了 30%。此外，对未使用和使用过滤器的每种蛋白质的 TPR 进行两两比较，结果平均提高了 1.7。该方法被实施到一个可供公众免费使用的网络服务器中。此实现的目的是为 3D 结构预测器提供一种工具，该工具可以通过满足最大数量的预测接触来帮助对替代模型进行排名，并且可以在结构已知的情况下提供接触的置信度得分。
Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM) method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins. Here we report a new implementation of the CM method with an added set of selection rules (filters). The parameters of the algorithm were optimized against fifteen high resolution crystal structures with optimization criterion that maximized the confidentiality of the predictions. The optimization resulted in a true positive ratio (TPR) of 0.08 for the CM without filters and a TPR of 0.14 for the CM with filters. The protocol was further benchmarked against 65 high resolution structures that were not included in the optimization test. The benchmarking resulted in a TPR of 0.07 for the CM without filters and to a TPR of 0.09 for the CM with filters. Thus, the inclusion of selection rules resulted to an overall improvement of 30%. In addition, the pair-wise comparison of TPR for each protein without and with filters resulted in an average improvement of 1.7. The methodology was implemented into a web server that is freely available to the public. The purpose of this implementation is to provide the 3D structure predictors with a tool that can help with ranking alternative models by satisfying the largest number of predicted contacts, as well as it can provide a confidence score for contacts in cases where structure is known.
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影响因子：
64.5
作者：
Shulman, AI;Larson, C;Ranganathan, R
通讯作者：
Ranganathan, R
DOI：
10.1038/nsb881
发表时间：
2003-01-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
--
作者：
Süel, GM;Lockless, SW;Ranganathan, R
通讯作者：
Ranganathan, R
影响因子：
6.8
作者：
Valencia, A;Pazos, F
通讯作者：
Pazos, F
影响因子：
5.8
作者：
Li, WZ;Jaroszewski, L;Godzik, A
通讯作者：
Godzik, A
影响因子：
5.6
作者：
Pazos, F;HelmerCitterich, M;Valencia, A
通讯作者：
Valencia, A