VADAR：一个用于蛋白质结构质量定量评估的网络服务器。
VADAR: a web server for quantitative evaluation of protein structure quality.
作者信息
Willard Leigh, Ranjan Anuj, Zhang Haiyan, Monzavi Hassan, Boyko Robert F, Sykes Brian D, Wishart David S
机构信息
Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2N8, Canada.
出版信息
Nucleic Acids Res. 2003 Jul 1;31(13):3316-9. doi: 10.1093/nar/gkg565.
Abstract
VADAR (Volume Area Dihedral Angle Reporter) is a comprehensive web server for quantitative protein structure evaluation. It accepts Protein Data Bank (PDB) formatted files or PDB accession numbers as input and calculates, identifies, graphs, reports and/or evaluates a large number (>30) of key structural parameters both for individual residues and for the entire protein. These include excluded volume, accessible surface area, backbone and side chain dihedral angles, secondary structure, hydrogen bonding partners, hydrogen bond energies, steric quality, solvation free energy as well as local and overall fold quality. These derived parameters can be used to rapidly identify both general and residue-specific problems within newly determined protein structures. The VADAR web server is freely accessible at http://redpoll.pharmacy.ualberta.ca/vadar.
摘要
VADAR（体积面积二面角报告器）是一个用于蛋白质结构定量评估的综合网络服务器。它接受蛋白质数据库（PDB）格式的文件或PDB登录号作为输入，并计算、识别、绘制图表、报告和/或评估大量（>30个）关键结构参数，这些参数既针对单个残基，也针对整个蛋白质。这些参数包括排除体积、可及表面积、主链和侧链二面角、二级结构、氢键伙伴、氢键能量、空间质量、溶剂化自由能以及局部和整体折叠质量。这些派生参数可用于快速识别新确定的蛋白质结构中的一般问题和残基特异性问题。可通过http://redpoll.pharmacy.ualberta.ca/vadar免费访问VADAR网络服务器。
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