CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.
CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.
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CPORT：一个共识接口预测器及其在与HADDOCK的预测驱动对接中的性能。
DOI：
10.1371/journal.pone.0017695
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发表时间：
2011-03-25
期刊：
影响因子：
3.7
通讯作者：
Bonvin AM
中科院分区：
文献类型：
--
作者：
de Vries SJ;Bonvin AM
大分子复合物是细胞的分子机器。原子层面的知识对于理解和影响它们的功能至关重要。然而，它们的数量是巨大的，并且使用经典的结构方法如NMR和X射线晶体学来研究它们的重要部分是极其困难的。因此，大规模计算方法在结构生物学中的重要性是显而易见的。本研究结合了两个这些计算方法，界面预测和对接，以获得蛋白质-蛋白质复合物的原子级结构，从它们的未结合的组件。在这里，我们将联合收割机六个界面预测Web服务器组合成一个共识方法，称为CPORT（瞬时复合物中界面残留物的共识预测）。我们表明，CPORT提供了更稳定和可靠的预测比每个单独的预测。一个协议被开发到我们的数据驱动的对接程序HADDOCK集成CPORT预测。对于实验信息有限的情况下，这种预测驱动的对接协议提出了一种替代从头对接，对接的复合物，而不使用任何信息。预测驱动的对接是在大量不同的蛋白质-蛋白质复合物上以盲态进行的。我们的研究结果表明，HADDOCK-CPORT组合的性能是有竞争力的ZDOCK-ZRANK，一个国家的最先进的从头对接/评分组合。最后，通过界面后预测（对接解决方案的接触分析）可以进一步改进原始界面预测。目前的研究表明，盲目的，预测驱动的对接使用CPORT和HADDOCK从头对接方法的竞争力。这是令人鼓舞的，因为预测驱动对接代表了数据驱动对接的绝对底线：任何额外的生物学知识都将大大改善预测驱动对接所获得的结果。最后，原始界面预测可以通过界面后预测进一步改进的事实表明，预测驱动的对接尚未被推到极限。CPORT的网络服务器可在http://haddock.chem.uu.nl/services/CPORT上免费获得。
Macromolecular complexes are the molecular machines of the cell. Knowledge at the atomic level is essential to understand and influence their function. However, their number is huge and a significant fraction is extremely difficult to study using classical structural methods such as NMR and X-ray crystallography. Therefore, the importance of large-scale computational approaches in structural biology is evident. This study combines two of these computational approaches, interface prediction and docking, to obtain atomic-level structures of protein-protein complexes, starting from their unbound components. Here we combine six interface prediction web servers into a consensus method called CPORT (Consensus Prediction Of interface Residues in Transient complexes). We show that CPORT gives more stable and reliable predictions than each of the individual predictors on its own. A protocol was developed to integrate CPORT predictions into our data-driven docking program HADDOCK. For cases where experimental information is limited, this prediction-driven docking protocol presents an alternative to ab initio docking, the docking of complexes without the use of any information. Prediction-driven docking was performed on a large and diverse set of protein-protein complexes in a blind manner. Our results indicate that the performance of the HADDOCK-CPORT combination is competitive with ZDOCK-ZRANK, a state-of-the-art ab initio docking/scoring combination. Finally, the original interface predictions could be further improved by interface post-prediction (contact analysis of the docking solutions). The current study shows that blind, prediction-driven docking using CPORT and HADDOCK is competitive with ab initio docking methods. This is encouraging since prediction-driven docking represents the absolute bottom line for data-driven docking: any additional biological knowledge will greatly improve the results obtained by prediction-driven docking alone. Finally, the fact that original interface predictions could be further improved by interface post-prediction suggests that prediction-driven docking has not yet been pushed to the limit. A web server for CPORT is freely available at http://haddock.chem.uu.nl/services/CPORT.
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DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL
影响因子：
2.9
作者：
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通讯作者：
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影响因子：
5.6
作者：
Fernández-Recio, J;Totrov, M;Abagyan, R
通讯作者：
Abagyan, R
影响因子：
2.9
作者：
Chen, HL;Zhou, HX
通讯作者：
Zhou, HX
影响因子：
2.9
作者：
Chen, R;Li, L;Weng, ZP
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Weng, ZP