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首页> 外文期刊>Journal of Molecular Biology >OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing
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OPUS-PSP: An orientation-dependent statistical all-atom potential derived from side-chain packing

机译：OPUS-PSP：来自侧链堆积的取向相关的统计全原子电势

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摘要

Here we report an orientation-dependent statistical all-atom potential derived from side-chain packing, named OPUS-PSP. It features a basis set of 19 rigid-body blocks extracted from the chemical structures of all 20 amino acid residues. The potential is generated from the orientation-specific packing statistics of pairs of those blocks in a non-redundant structural database. The purpose of such an approach is to capture the essential elements of orientation dependence in molecular packing interactions. Tests of OPUS-PSP on commonly used decoy sets demonstrate that it Significantly outperforms most of the existing knowledge-based potentials in terms of both its ability to recognize native structures and consistency in achieving high Z-scores across decoy sets. As OPUS-PSP excludes interactions among main-chain atoms, its success highlights the crucial importance of side-chain packing in forming native protein structures. Moreover, OPUS-PSP does not explicitly include solvation terms, and thus the potential should perform well when the solvation effect is difficult to determine, such as in membrane proteins. Overall, OPUS-PSP is a generally applicable potential for protein structure modeling, especially for handling side-chain conformations, one of the most difficult steps in high-accuracy protein structure prediction and refinement. (C) 2007 Elsevier Ltd. All rights reserved.
机译：在这里，我们报告了衍生自侧链包装的取向依赖性统计全原子电势，称为OPUS-PSP。它具有从所有20个氨基酸残基的化学结构中提取的19个刚体嵌段的基础集。势是从非冗余结构数据库中的这些块对的定向特定的装箱统计数据生成的。这种方法的目的是捕获分子堆积相互作用中取向依赖性的基本要素。 OPUS-PSP在常用诱饵集上的测试表明，就其识别原始结构的能力和在整个​​诱饵集上获得高Z分数的一致性而言，它明显优于大多数现有的基于知识的潜力。由于OPUS-PSP排除了主链原子之间的相互作用，其成功突出了侧链堆积在形成天然蛋白质结构中的至关重要性。此外，OPUS-PSP没有明确包括溶剂化术语，因此，当难以确定溶剂化效果（例如在膜蛋白中）时，电势应表现良好。总体而言，OPUS-PSP在蛋白质结构建模中具有普遍适用的潜力，特别是在处理侧链构象方面，这是高精度蛋白质结构预测和改进中最困难的步骤之一。 （C）2007 Elsevier Ltd.保留所有权利。

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