Jumping low, jumping high: Controlling hopping in the protein energy surface

Brian S. Olson, Amarda Shehu
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Abstract

The protein conformational space is characterized as a multi-dimensional funnel-like energy surface with conformations corresponding to the native state around the energy basin. The dimensionally and ruggedness of this energy surface are primary why computationally determining the biologically active or native state of a protein remains a difficult challenge. A common template among structure prediction protocols begins by sampling many local minima in the energy surface. Basin Hopping (BH) has emerged as a suitable framework for effectively sampling these coarse grained local minima. BH consists of a series structural perturbations followed by minimizations, forming a trajectory of local minima with the Metropolis criterion biasing it towards increasingly low-energy minima.
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低跳、高跳:控制蛋白能量面跳跃
蛋白质构象空间的特征是一个多维的漏斗状能量面,其构象与能量盆周围的天然状态相对应。这种能量表面的尺寸和坚固性是计算确定蛋白质的生物活性或天然状态仍然是一项艰巨挑战的主要原因。在结构预测协议中,一个常用的模板是从能量表面的许多局部极小值采样开始的。盆地跳跃(BH)已成为有效采样这些粗粒度局部极小值的合适框架。黑洞由一系列结构扰动和最小化组成,形成了一个局部极小的轨迹,Metropolis准则使其趋向于越来越低能量的极小值。
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