Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein.
Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein.
复制标题
用于肽和微蛋白构象空间搜索的多重模拟退火分子动力学 (MSA-MD)
DOI：
10.1038/srep15568
复制
发表时间：
2015-10-23
影响因子：
4.6
通讯作者：
Yang GF
中科院分区：
文献类型：
--
作者：
Hao GF;Xu WF;Yang SG;Yang GF
蛋白质和多肽结构的预测对于了解它们的功能以及与其他分子的相互作用是至关重要的。然而，由于构象空间的粗糙拓扑结构和有限的模拟时间尺度，利用分子模拟技术直接从一级氨基酸序列预测多肽结构总是受到阻碍。我们开发了一种新的策略，称为多重模拟退火法-分子动力学(MSA-MD)来识别多肽和微小蛋白的天然状态。使用MSA-MD方法可以得到一组接近自然结构的簇，与连续MD和传统的SA-MD模拟相比，这种方法在获得自然结构方面明显更有效。
Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We developed here a new strategy, named Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to identify the native states of a peptide and miniprotein. A cluster of near native structures could be obtained by using the MSA-MD method, which turned out to be significantly more efficient in reaching the native structure compared to continuous MD and conventional SA-MD simulation.