Prediction of ligand binding affinity by the combination of replica-exchange method and double-decoupling method
Prediction of ligand binding affinity by the combination of replica-exchange method and double-decoupling method
复制标题
复制交换法和双解偶联法相结合预测配体结合亲和力
DOI：
10.1021/ct500539u
复制
发表时间：
2014
影响因子：
5.5
通讯作者：
and T. Tanaka
中科院分区：
文献类型：
--
作者：
Y. Okamoto;H. Kokubo;and T. Tanaka
提出了一种预测配体与蛋白质结合亲和力的方法。我们首先通过复制交换伞采样或其推广预测了蛋白质-配体复合物的结构。然后，我们计算配体结合亲和力的基础上，这些预测的配体-蛋白质结合结构的双重解耦方法。为了验证所提出方法的有效性，我们将其应用于癌蛋白MDM 2和配体的系统。预测的结合亲和力的值被证明是在良好的协议从实验。
A prediction method for ligand binding affinities to proteins is proposed. We first predict the structures of protein–ligand complex by the replica-exchange umbrella sampling or its extension. We then calculate ligand binding affinities based on these predicted ligand–protein bound structures by the double-decoupling method. As a test of the effectiveness of the proposed method, we applied it to the system of the oncoprotein MDM2 and a ligand. The value of the predicted binding affinity turned out to be in good agreement with that from experiments.