Pellegrini M, Doniach S
Department of Physics, Stanford University, California 94305-4090.
Proteins. 1993 Apr;15(4):436-44. doi: 10.1002/prot.340150410.
A Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicitly maximize surface contact, but minimizes the energy computed using coarse-grained pair potentials. The final refinement of our best solutions using all-atom OPLS potentials (Jorgensen and Tirado-Rives8) consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance-dependent dielectric function is an improvement over the more commonly used linear form.
开发了一种蒙特卡罗算法，用于搜索鸡蛋清溶菌酶与抗体的最佳对接构型。溶菌酶和抗体均保持刚性。与其他作者的工作不同，我们的算法并非试图明确最大化表面接触，而是使使用粗粒度对势计算的能量最小化。使用全原子OPLS势（乔根森和蒂拉多 - 里韦斯8）对我们的最佳解决方案进行最终优化，对于三种不同的抗体，始终产生天然构象作为首选解决方案。我们发现，使用指数距离依赖介电函数比更常用的线性形式有所改进。
