蛋白质结构预测
多序列比对
蛋白质结构
序列比对
计算机科学
侧链
计算生物学
残留物(化学)
同源建模
蛋白质测序
结构线形
生物系统
肽序列
化学
生物
生物化学
酶
有机化学
基因
聚合物
作者
Yu-Tung Chien,Shao-Wei Huang
出处
期刊:PLOS ONE
[Public Library of Science]
日期:2012-10-24
卷期号:7 (10): e47951-e47951
被引量:13
标识
DOI:10.1371/journal.pone.0047951
摘要
Prediction of protein catalytic residues provides useful information for the studies of protein functions. Most of the existing methods combine both structure and sequence information but heavily rely on sequence conservation from multiple sequence alignments. The contribution of structure information is usually less than that of sequence conservation in existing methods. We found a novel structure feature, residue side chain orientation, which is the first structure-based feature that achieves prediction results comparable to that of evolutionary sequence conservation. We developed a structure-based method, Enzyme Catalytic residue SIde-chain Arrangement (EXIA), which is based on residue side chain orientations and backbone flexibility of protein structure. The prediction that uses EXIA outperforms existing structure-based features. The prediction quality of combing EXIA and sequence conservation exceeds that of the state-of-the-art prediction methods. EXIA is designed to predict catalytic residues from single protein structure without needing sequence or structure alignments. It provides invaluable information when there is no sufficient or reliable homology information for target protein. We found that catalytic residues have very special side chain orientation and designed the EXIA method based on the newly discovered feature. It was also found that EXIA performs well for a dataset of enzymes without any bounded ligand in their crystallographic structures.
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