使用MODELLER进行比较蛋白质结构建模。
Comparative Protein Structure Modeling Using MODELLER.
作者信息
Webb Benjamin, Sali Andrej
机构信息
University of California at San Francisco, San Francisco, California.
出版信息
Curr Protoc Bioinformatics. 2016 Jun 20;54:5.6.1-5.6.37. doi: 10.1002/cpbi.3.
Abstract
Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.
摘要
比较蛋白质结构建模主要基于给定蛋白质序列（目标序列）与一种或多种已知结构的蛋白质（模板）的比对来预测其三维结构。预测过程包括折叠类型确定、目标序列与模板的比对、模型构建和模型评估。本单元描述了如何使用MODELLER程序计算比较模型以及如何使用此类模型的ModBase数据库，并讨论了比较建模的所有四个步骤、常见错误和一些应用。以阴道毛滴虫乳酸脱氢酶（TvLDH）的建模为例进行了说明。还介绍了MODELLER软件的下载和安装。© 2016约翰威立国际出版公司。
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