STATUS OF EMPIRICAL METHODS FOR PREDICTION OF PROTEIN BACKBONE TOPOGRAPHY
STATUS OF EMPIRICAL METHODS FOR PREDICTION OF PROTEIN BACKBONE TOPOGRAPHY
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DOI：
10.1021/bi00668a030
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发表时间：
1976-01-01
期刊：
影响因子：
2.9
通讯作者：
SCHERAGA, HA
中科院分区：
文献类型：
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作者：
MAXFIELD, FR;SCHERAGA, HA
描述了一种经验预测算法，该算法使用 20 种蛋白质中的短程（残基内）和中程（两侧最多 4 个邻居）相互作用的信息，将蛋白质中的每个残基分配给 5 种构象状态中的一种。构象状态是根据残基的主链二面角来定义的，以便预测算法可用于生成后续能量最小化程序的起始构象，这对于预测蛋白质的3维结构是必要的。对描述蛋白质中短程和中程相互作用的影响的参数的确定中的统计误差进行估计。这种统计误差在限制所有依赖于已知结构蛋白质数据的预测方法的准确性方面发挥着重要作用。使用所描述的方法，20 种蛋白质中 56% 的残基被正确分配到 5 种构象状态中的一种。似乎任何预测方法都不太可能显着提高将残基分配给特定主链构象的准确性，除非数据库的大小大大增加。
An empirical prediction algorithm which uses information on the short-range (intraresidue) and medium-range (up to 4 neighbors on either side) interactions in 20 proteins to assign every residue in a protein to 1 of 5 conformational states is described. The conformational states are defined in terms of the backbone dihedral angles of the residue so that the prediction algorithm can be used to generate starting conformations for subsequent energy-minimization procedures, which would be necessary to predict the 3-dimensional structure of a protein. An estimate is made of the statistical error in the determination of the parameters describing the effects of short-range and medium-range interactions in proteins. This statistical error plays a large role in limiting the accuracy of all prediction methods which rely on data from proteins of known structure. Using the method described, 56% of the residues in 20 proteins were assigned correctly to 1 of 5 conformational states. It seems unlikely that any prediction method can significantly improve on this accuracy for assigning residues to specific backbone conformations unless the size of the data base is increased greatly.