PELE: Protein energy landscape exploration. A novel Monte Carlo based technique
PELE: Protein energy landscape exploration. A novel Monte Carlo based technique
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DOI：
10.1021/ct0501811
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发表时间：
2005-11-01
影响因子：
5.5
通讯作者：
Guallar, V
中科院分区：
文献类型：
--
作者：
Borrelli, KW;Vitalis, A;Guallar, V
结合蛋白质结构预测算法和 metropolis蒙特卡洛技术，我们提供了一种探索全原子能量景观的新方法。该技术的核心是基于导向局部扰动，随后进行侧链采样以及最小化循环。这里介绍了该算法及其在配体扩散中的应用。针对包含不同大小配体的不同系统，成功地模拟了配体退出途径：肌红蛋白中的一氧化碳、细胞色素P450cam中的樟脑以及肠道脂肪酸结合蛋白中的棕榈酸。这些初步应用揭示了这种新技术在绘制毫秒时间尺度过程方面的潜力。与探索相关的计算成本明显低于传统分子动力学模拟。
Combining protein structure prediction algorithms and Metropolis Monte Carlo techniques, we provide a novel method to explore all-atom energy landscapes. The core of the technique is based on a steered localized perturbation followed by side-chain sampling as well as minimization cycles. The algorithm and its application to ligand diffusion are presented here. Ligand exit pathways are successfully modeled for different systems containing ligands of various sizes: carbon monoxide in myoglobin, camphor in cytochrome P450cam, and palmitic acid in the intestinal fatty-acid-binding protein. These initial applications reveal the potential of this new technique in mapping millisecond-time-scale processes. The computational cost associated with the exploration is significantly less than that of conventional MD simulations.