蛋白质微秒级折叠过程的快速模拟

doi:10.3976/j.issn.1002-4026.2015.03.018

Abstract

Abstract: We performed molecular dynamics simulation for four proteins, CLN025 (2ZEI), MHA6 (2I9M), 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  for protein 2ZEI, 0.191 μs and 1.142 for protein 219M, 4.23 μs and 1.37  for protein Villin, and 2.49 μs and 0.63  protein TrpCage.It demonstrates that microsecond level protein folding simulation can be implemented on a desktop workstation with GPU computing.

Key words: protein folding, GBNeck2, ff12SB force field, GPU computing, molecular dynamics

CLC Number:

O641.12

LIN Yun, ZHANG Shaolong,ZHANG Qinggang, ZHANG Yici. Rapid simulation of protein microsecond level folding process[J].SHANDONG SCIENCE, 2015, 28(3): 96-103.

References

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Rapid simulation of protein microsecond level folding process

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