Aqvist J, Medina C, Samuelsson J E
Department of Molecular Biology, Uppsala University, Sweden.
Protein Eng. 1994 Mar;7(3):385-91. doi: 10.1093/protein/7.3.385.
A new semi-empirical method for calculating free energies of binding from molecular dynamics (MD) simulations is presented. It is based on standard thermodynamic cycles and on a linear approximation of polar and non-polar free energy contributions from the corresponding MD averages. The method is tested on a set of endothiapepsin inhibitors and found to give accurate results both for absolute as well as relative free energies.
本文提出了一种通过分子动力学（MD）模拟计算结合自由能的新的半经验方法。该方法基于标准热力学循环以及相应MD平均值对极性和非极性自由能贡献的线性近似。该方法在一组内硫肽酶抑制剂上进行了测试，发现无论是绝对自由能还是相对自由能都能给出准确的结果。
