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首页> 外文期刊>Computational Biology and Bioinformatics, IEEE/ACM Transactions on >Residue-Specific Side-Chain Polymorphismsvia Particle Belief Propagation
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Residue-Specific Side-Chain Polymorphismsvia Particle Belief Propagation

机译：通过粒子信念传播的残基特异性侧链多态性

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摘要

Protein side chains populate diverse conformational ensembles in crystals. Despite much evidence that there is widespread conformational polymorphism in protein side chains, most of the X-ray crystallography data are modeled by single conformations in the Protein Data Bank. The ability to extract or to predict these conformational polymorphisms is of crucial importance, as it facilitates deeper understanding of protein dynamics and functionality. In this paper, we describe a computational strategy capable of predicting side-chain polymorphisms. Our approach extends a particular class of algorithms for side-chain prediction by modeling the side-chain dihedral angles more appropriately as continuous rather than discrete variables. Employing a new inferential technique known as particle belief propagation, we predict residue-specific distributions that encode information about side-chain polymorphisms. Our predicted polymorphisms are in relatively close agreement with results from a state-of-the-art approach based on X-ray crystallography data, which characterizes the conformational polymorphisms of side chains using electron density information, and has successfully discovered previously unmodeled conformations.
机译：蛋白质侧链在晶体中构成各种构象集合。尽管有大量证据表明蛋白质侧链中存在广泛的构象多态性，但大多数X射线晶体学数据都是通过蛋白质数据库中的单个构象建模的。提取或预测这些构象多态性的能力至关重要，因为它有助于更​​深入地了解蛋白质动力学和功能。在本文中，我们描述了一种能够预测侧链多态性的计算策略。我们的方法通过更适当地将侧链二面角建模为连续变量而不是离散变量，从而扩展了特定类别的侧链预测算法。利用一种称为粒子置信传播的新推理技术，我们可以预测残基特定的分布，该分布编码有关侧链多态性的信息。我们预测的多态性与基于X射线晶体学数据的最新方法的结果相对一致，该方法使用电子密度信息表征侧链的构象多态性，并成功地发现了以前未建模的构象。

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