On the energy components governing molecular recognition in the framework of continuum approaches.
On the energy components governing molecular recognition in the framework of continuum approaches.
复制标题
在连续方法框架中控制分子识别的能量成分上。
DOI：
10.3389/fmolb.2015.00005
复制
发表时间：
2015
影响因子：
5
通讯作者：
Alexov E
中科院分区：
文献类型：
--
作者：
Li L;Wang L;Alexov E
分子识别是将多个生物大分子聚集在一起形成络合物的过程，其最重要的特征之一就是结合自由能。在已知结合和非结合分子的三维结构的情况下，存在多种方法来模拟结合自由能。其中，连续体方法因其计算效率高，同时又能提供相当准确的预测而颇具吸引力。在这里，我们回顾了该领域的最新发展，强调了对绑定时发生的物理过程进行适当描述的重要性。特别是，我们专注于旨在将结合现象的一些原子细节捕捉到连续统框架中的努力。在可能的情况下，对能源组成部分进行相互独立的审查。然而，有人指出，严格的方法应该考虑同一镜头上的所有能量贡献。还概述了利用单个能量分量预测结合亲和力的两种主要方案。
Molecular recognition is a process that brings together several biological macromolecules to form a complex and one of the most important characteristics of the process is the binding free energy. Various approaches exist to model the binding free energy, provided the knowledge of the 3D structures of bound and unbound molecules. Among them, continuum approaches are quite appealing due to their computational efficiency while at the same time providing predictions with reasonable accuracy. Here we review recent developments in the field emphasizing on the importance of adopting adequate description of physical processes taking place upon the binding. In particular, we focus on the efforts aiming at capturing some of the atomistic details of the binding phenomena into the continuum framework. When possible, the energy components are reviewed independently of each other. However, it is pointed out that rigorous approaches should consider all energy contributions on the same footage. The two major schemes for utilizing the individual energy components to predict binding affinity are outlined as well.