用界面几何约束的多起点蒙特卡罗方法对蛋白质/ 短肽识别体系的对接计算

提出了一个界面几何约束的多起点蒙特卡罗构象搜索方法，并把这个方法用于三个丝氨酸蛋白酶/短肽抑制剂体系的刚性、部分柔性和全部柔性对接计算中。我们的方法成功地预测出了接近晶体结构的配体构象。与没有几何约束相比，我们的几何约束蒙特卡罗方法显示出了更好的收敛性质。

Docking of protein-peptide segment complexes with multi-start monte carlo procedure restrained by surface geometry match

A multi-start Monte Carlo procedure restrained by surface geometry match is presented and used to dock three serine protease-peptide segment systems. For each of the ligands, one hundred of initial conformations, which meet given steric and geometric tolerances, are selected randomly. Each of the initial conformations is optimized by a local Monte Carlo procedure which makes a step to a new random step along with the routine of reduction of the radius of gyration Rg of protein-ligand complex according to a given probability. The random step is followed by a local minimization in the total conformational spaces. The radius of gyration Rg of protein- ligand complex characters the quality of geometric fit. Small Rg value corresponds to compact packing and good fit of geometry on the interface. The algorithm successfully prddicts the conformations of ligands close to the crystal structures for the three test systems in the docking of rigidity, partial flexibility and total flexibility and the runs display much better convergence properties than the procedure without the guide of geometric fit.