An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
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DOI：
10.1006/jmbi.1997.1479
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发表时间：
1998-02-06
影响因子：
5.6
通讯作者：
Moult, J
中科院分区：
文献类型：
--
作者：
Samudrala, R;Moult, J
我们提出了一种形式主义来计算的概率的氨基酸序列构象是天然的，给定一组成对的原子-原子距离。的形式主义是用来获得三个歧视性的功能与不同类型的表示观察到的原子-原子接触的蛋白质结构的数据库。这些函数包括两个虚原子表示和一个全重原子表示。当应用到六个不同的诱饵集包含一系列正确和不正确的构象的氨基酸序列，全原子距离依赖的歧视功能是能够识别正确的不正确的，往往比歧视功能，使用近似表示。我们说明了使用一个详细的原子描述获得最准确的歧视的重要性，以及测试歧视功能对各种各样的诱饵的必要性。的歧视性功能也被证明是能够捕捉原子原子的偏好的细节。这些结果表明，全原子距离依赖的判别函数将是有用的蛋白质结构预测和模型改进。(C)出版社：Academic Press Limited。
We present a formalism to compute the probability of an amino acid sequence conformation being native-like, given a set of pairwise atom-atom distances. The formalism is used to derive three discriminatory functions with different types of representations for the atom-atom contacts observed in a database of protein structures. These functions include two virtual atom representations and one all-heavy atom representation. When applied to six different decoy sets containing a range of correct and incorrect conformations of amino acid sequences, the all-atom distance-dependent discriminatory function is able to identify correct from incorrect more often than the discriminatory functions using approximate representations. We illustrate the importance of using a detailed atomic description for obtaining the most accurate discrimination, and the necessity for testing discriminatory functions against a wide variety of decoys. The discriminatory function is also shown to be capable of capturing the fine details of atom-atom preferences. These results suggest that the all-atom distance-dependent discriminatory function will be useful for protein structure prediction and model refinement. (C) 1998 Academic Press Limited.