Marelius J, Kolmodin K, Feierberg I, Aqvist J
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Sweden.
J Mol Graph Model. 1998 Aug-Dec;16(4-6):213-25, 261. doi: 10.1016/s1093-3263(98)80006-5.
A new molecular dynamics program for free energy calculations in biomolecular systems is presented. It is principally designed for free energy perturbation simulations, empirical valence bond calculations, and binding affinity estimation by linear interaction energy methods. Evaluation of ligand-binding selectivity and free energy profiles for nucleophile activation in two protein tyrosine phosphatases as well as absolute binding affinity estimation for a lysine-binding protein are given as examples.
本文介绍了一种用于生物分子系统自由能计算的新分子动力学程序。它主要设计用于自由能微扰模拟、经验价键计算以及通过线性相互作用能方法估算结合亲和力。以评估两种蛋白质酪氨酸磷酸酶中配体结合选择性和亲核试剂活化的自由能分布以及赖氨酸结合蛋白的绝对结合亲和力为例进行了说明。
