Department of Pharmacy, University of Pisa , 56126 Pisa, Italy.
J Chem Inf Model. 2014 Oct 27;54(10):2980-6. doi: 10.1021/ci500424n. Epub 2014 Sep 18.
Molecular docking strategies are one of the most widely used techniques for predicting the binding mode of a ligand and for obtaining new hits in virtual screening studies. In order to improve the accuracy of this approach, we tested the reliability of applying a consensus docking protocol by combining ten different docking procedures. The analysis was carried out in terms of consensus cross-docking and by using an enriched database. The results highlight that from a qualitative point of view consensus docking is able to predict the ligand binding pose better than the single docking programs and is also able to give hints concerning the reliability of the docking pose. With regard to the virtual screening studies, consensus docking was evaluated for three different targets of the Directory of Useful Decoys (DUD), and the obtained results suggest that this approach performs as well as the best available methods found in the literature, therefore supporting the idea that this procedure can be profitably applied for the identification of new hits.
分子对接策略是预测配体结合模式和在虚拟筛选研究中获得新命中的最广泛使用的技术之一。为了提高这种方法的准确性，我们通过结合十种不同的对接程序来测试应用共识对接协议的可靠性。该分析是根据共识交叉对接和使用富集数据库进行的。结果表明，从定性的角度来看，共识对接能够比单个对接程序更好地预测配体结合构象，并且还能够提供关于对接构象可靠性的提示。关于虚拟筛选研究，共识对接针对目录有用诱饵（DUD）的三个不同靶标进行了评估，结果表明该方法的性能与文献中发现的最佳可用方法相当，因此支持这样的观点，即该方法可以成功应用于识别新的命中。
