Chinea G, Padron G, Hooft R W, Sander C, Vriend G
Center for Genetic Engineering and Biotechnology, Havana, Cuba.
Proteins. 1995 Nov;23(3):415-21. doi: 10.1002/prot.340230315.
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.
在本研究中，我们专注于将替换侧链作为同源性建模的一个子任务。出现了两个问题。如何确定潜在的低能旋转异构体？以及如何避免因预测出多个良好旋转异构体的多个残基组合而导致的组合爆炸？我们试图通过选择位置特异性而非广义的旋转异构体，以及根据残基在旋转异构体空间中的自由度对必须建模的残基进行排序来解决这些问题。我们方法的实际优点在于，对于主链相似度高的情况，模型质量良好，所需的人工干预量少，以及该方法能自动估计每个残基建模的可靠性。如果需要对大的主链重排或环插入及缺失进行建模，本期所描述的其他方法可能更合适。
