EVALUATION OF COMPARATIVE PROTEIN MODELING BY MODELER
EVALUATION OF COMPARATIVE PROTEIN MODELING BY MODELER
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DOI：
10.1002/prot.340230306
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发表时间：
1995-11-01
期刊：
影响因子：
--
通讯作者：
KARPLUS, M
中科院分区：
文献类型：
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作者：
SALI, A;POTTERTON, L;KARPLUS, M
我们评估了人核苷二磷酸激酶，小鼠细胞视黄酸结合蛋白I和人嗜酸性粒细胞神经毒素的3D模型，这些模型是由Modeller计算的，该程序是一种通过空间限制来满足的比较蛋白质建模的程序。这些模型具有良好的立体化学化学，至少与晶体学结构一样相似，与最接近的模板结构一样，最大的误差发生在未正确对齐或模板结构与正确结构不相似的区域中。这些区域主要对应于暴露的环，任何长度的插入和未经保密的侧链，当具有超过40％序列身份的模板结构可用于目标蛋白时，该模型可能具有约90％的主链。在很大程度上以X射线结构为X射线结构的RMS偏差在很大程度上以X射线结构为单位，因为模板可能与目标的X射线结构相似，因此该RMS类似偏差与同一蛋白质的精制NMR和X射线晶体学结构之间的总体差异相当。 （c）1995 Wiley-Liss，Inc。
We evaluate 3D models of human nucleoside diphosphate kinase, mouse cellular retinoic acid binding protein I, and human eosinophil neurotoxin that were calculated by MODELLER, a program for comparative protein modeling by satisfaction of spatial restraints. The models have good stereochemistry and are at least as similar to the crystallographic structures as the closest template structures, The largest errors occur in the regions that were not aligned correctly or where the template structures are not similar to the correct structure. These regions correspond predominantly to exposed loops, insertions of any length, and non-conserved side chains, When a template structure with more than 40% sequence identity to the target protein is available, the model is likely to have about 90% of the mainchain atoms modeled with an rms deviation from the X-ray structure of approximate to 1 Angstrom in large part because the templates are likely to be that similar to the X-ray structure of the target, This rms deviation is comparable to the overall differences between refined NMR and X-ray crystallography structures of the same protein. (C) 1995 Wiley-Liss, Inc.