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首页> 外文期刊>The Journal of Chemical Physics >Multisequence algorithm for coarse-grained biomolecular simulations: Exploring the sequence-structure relationship of proteins
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Multisequence algorithm for coarse-grained biomolecular simulations: Exploring the sequence-structure relationship of proteins

机译：粗粒生物分子模拟的多仪算法：探索蛋白质的序列结构关系

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摘要

We consider a generalized-ensemble algorithm for coarse-grained simulations of biomolecules which allows the thermodynamic behavior of two or more sequences to be determined in a single multisequence run. By carrying out a random walk in sequence space, the method also enhances conformational sampling. Escape from local energy minima is accelerated by visiting sequences for which the minima are more shallow or absent. We test the method on an intermediate-resolution coarse-grained model for protein folding with 3 amino acid types and explore the potential for a large-scale coverage of sequence space by applying the method to sets of more than 1000 sequences. The resulting thermodynamic data are used to analyze the structures and stability properties of sequences covering the space between folds with different secondary structures. Published by AIP Publishing.
机译：我们考虑用于粗粒模拟的生物分子的广义集合算法，其允许在单个多音节运行中确定两个或更多个序列的热力学行为。 通过在序列空间进行随机步行，该方法还增强了构象采样。 通过访问序列加速来自局部能量最小值的逃避，该序列更浅或不存在。 我们在用3种氨基酸类型的蛋白质折叠的中间分辨率粗粒模型中测试该方法，并通过将方法应用于超过1000个序列，探索序列空间的大规模覆盖的可能性。 得到的热力学数据用于分析覆盖具有不同二级结构折叠之间的空间的序列的结构和稳定性。 通过AIP发布发布。

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