THE USE OF POSITION-SPECIFIC ROTAMERS IN MODEL-BUILDING BY HOMOLOGY
THE USE OF POSITION-SPECIFIC ROTAMERS IN MODEL-BUILDING BY HOMOLOGY
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DOI：
10.1002/prot.340230315
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发表时间：
1995-11-01
期刊：
影响因子：
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通讯作者：
VRIEND, G
中科院分区：
文献类型：
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作者：
CHINEA, G;PADRON, G;VRIEND, G
在这项研究中，我们集中在取代侧链作为一个子任务的模型建设同源。出现了两个问题。如何确定潜在的低能转子？如何避免多残基组合所产生的组合爆炸，而多残基组合所预测的是多个好的转子。我们试图通过选择特定位置的旋转体而不是广义的旋转体来解决这些问题，并通过将残数分类，这些残数必须被建模为旋转体空间中自由度的函数。我们的方法的实际优点是高主干相似度情况下的模型质量，所需的人工干预量少，以及该方法自动估计每个残基建模的可靠性。如果需要对大型主干重排或循环插入和删除进行建模，本问题中描述的其他方法可能更合适。(C) 1995 Wiley-Liss, Inc。
In this study we concentrate on replacing side chains as a subtask of model building by homology. Two problems arise. How to determine potential low energy rotamers? And how to avoid the combinatorial explosion that results from the combination of many residues for which multiple good rotamers are predicted? We attempt to solve these problems by choosing position-specific rather than generalized rotamers and by sorting the residues that have to be modelled as a function of their freedom in rotamer space. The practical advantages of our method are the quality of the models for cases of high backbone similarity, the small amount of human intervention needed, and the fact that the method automatically estimates the reliability with which each residue has been modeled. Other methods described in this issue are probably more suitable if large backbone rearrangements or loop insertions and deletions need to be modeled. (C) 1995 Wiley-Liss, Inc.