Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function.
Modeling CAPRI targets 110-120 by template-based and free docking using contact potential and combined scoring function.
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DOI：
10.1002/prot.25380
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发表时间：
2018-03
期刊：
影响因子：
2.9
通讯作者：
Vakser IA
中科院分区：
文献类型：
--
作者：
Kundrotas PJ;Anishchenko I;Badal VD;Das M;Dauzhenka T;Vakser IA
本文介绍了我们在 CASP12/CAPRI37 联合轮中基于模板和自由对接预测的分析。开发了基于模板对接的新评分函数，以 Dockground 资源为基准，并将其应用于目标。结果表明，该函数成功区分了不正确的对接预测。在正确预测的目标中，评分函数还需要考虑其他因素，例如模板之间寡聚状态的一致性、生物功能的相似性、生物界面相关性等。评分函数仍然不能很好地区分生物界面和晶体堆积界面，并且需要进一步开发以实现α-螺旋束的对接。对于三聚体靶标，尽管结构相似，但基于序列的方法没有找到通用模板，这表明在比较对接中互补使用基于结构和基于序列的比对。结果表明，如果找到良好的对接模板，即使从很大程度上不准确的各个子单元模型中也可以构建准确的界面模型。然而，自由对接对各个模型的质量非常敏感。然而，我们新开发的接触电位检测到了结合位点的大致位置。
The paper presents analysis of our template-based and free docking predictions in the joint CASP12/CAPRI37 round. A new scoring function for template-based docking was developed, benchmarked on the Dockground resource, and applied to the targets. The results showed that the function successfully discriminates the incorrect docking predictions. In correctly predicted targets, the scoring function was complemented by other considerations, such as consistency of the oligomeric states among templates, similarity of the biological functions, biological interface relevance, etc. The scoring function still does not distinguish well biological from crystal packing interfaces, and needs further development for the docking of bundles of α-helices. In the case of the trimeric targets, sequence-based methods did not find common templates, despite similarity of the structures, suggesting complementary use of structure- and sequence-based alignments in comparative docking. The results showed that if a good docking template is found, an accurate model of the interface can be built even from largely inaccurate models of individual subunits. Free docking however is very sensitive to the quality of the individual models. However, our newly developed contact potential detected approximate locations of the binding sites.
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影响因子：
3
作者：
Krieger E;Vriend G
通讯作者：
Vriend G
影响因子：
5.6
作者：
Guerois, R;Nielsen, JE;Serrano, L
通讯作者：
Serrano, L
影响因子：
6.8
作者：
Buchete, NV;Straub, JE;Thirumalai, D
通讯作者：
Thirumalai, D
影响因子：
5.6
作者：
Park, B;Levitt, M
通讯作者：
Levitt, M
DOI：
10.1073/pnas.1200678109
发表时间：
2012-06-12
影响因子：
11.1
作者：
Kundrotas, Petras J.;Zhu, Zhengwei;Vakser, Ilya A.
通讯作者：
Vakser, Ilya A.