Karney Charles F F, Ferrara Jason E, Brunner Stephan
Sarnoff Corporation, Princeton, New Jersey 08543-5300, USA.
J Comput Chem. 2005 Feb;26(3):243-51. doi: 10.1002/jcc.20167.
A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move, which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding site is known, and that an accurate chemical force field together with a continuum solvation model is used, this method provides a quantitative estimate of the free energy of binding.
给出了一种用于计算配体与蛋白质结合亲和力的蒙特卡罗方法。该方法涉及通过一个离散变量扩展构型空间，该变量指示配体是否与蛋白质结合，以及一种特殊的蒙特卡罗移动，它允许在未结合状态和结合状态之间进行转变。只要给出准确的蛋白质结构，已知蛋白质-配体结合位点，并且使用准确的化学力场和连续溶剂化模型，该方法就能提供结合自由能的定量估计。
