蛋白质微秒级折叠过程的快速模拟

Rapid simulation of protein microsecond level folding process

使用ff12SB力场和广义玻恩(GB-Neck2)隐性水模型在GTX670 GPU上对4个蛋白质CLN025(2ZEI)、MHA6(2I9M)、Trp-Cage(1L2Y)、Villin(3TRW)的微秒级折叠过程进行了分子动力学模拟,2ZEI的折叠时间和均方根偏差为5.94μs和0.897,2I9M的折叠时间和均方根偏差为0.191μs和1.142,Villin的折叠时间和均方根偏差为4.23μs和1.37,Trp-Cage的折叠时间和均方根偏差为2.48μs和0.63。结果表明,蛋白质折叠模拟已经能够通过GPU计算在桌面计算机上实现。

We performed molecular dynamics simulation for four proteins, CLN025 （2ZEI）, MHA6 （219M）, Trp-Cage （1L2Y） and Villin （3TRW） on GEX670-GPU.with AMBER ff12SB force field and Generalized Born （GB-Neck2） implicit solvent model. Results show that folding time and RMSD compared to its crystal structure are 5.94 μS and 0. 897 A for protein 2ZEI, 0. 191 μs and 1. 142 A for protein 219M, 4.23 μs and 1. 37 A, for protein Villin, and 2.49 μs and 0.63/k protein Trp-Cage. It demonstrates that microsecond level protein folding simulation can be implemented on a desktop workstation with GPU computing.