UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.
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DOI：
10.1093/nar/gky328
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发表时间：
2018-07-02
影响因子：
14.9
通讯作者：
Liwo A
中科院分区：
文献类型：
--
作者：
Czaplewski C;Karczynska A;Sieradzan AK;Liwo A
给出了UNRES程序包(http://www.unres.pl))的服务器实现，该程序用于粗粒度模拟蛋白质结构和基于物理的UNRES模型，称为UNRES服务器。与大多数蛋白质粗粒度模型不同，由于其基于物理的起源，UNRES力场可以用于模拟，包括那些针对蛋白质结构预测的模拟，而不需要来自结构数据库的辅助信息；然而，实施包括使用约束的可能性。目前的UNRES服务器可以运行局部能量最小化、正则分子动力学模拟、副本交换和多重副本交换分子动力学模拟，后者适用于蛋白质结构预测。用户提供的输入包括蛋白质序列和可选的来自二级结构预测或小X射线散射数据的约束，以及选择或键入的模拟类型和参数。低聚蛋白质，以及那些含有D-氨基酸残基和二硫键的蛋白质可以被处理。输出以图形方式显示(最小化结构、轨迹、最终模型、轨迹/总体分析)；但是，用户可以下载所有输出文件。UNRES服务器可在http://unres-server.chem.ug.edu.pl.上免费访问
A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.
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影响因子：
3.3
作者：
Khalili, M;Liwo, A;Scheraga, HA
通讯作者：
Scheraga, HA
影响因子：
3.3
作者：
Rojas, Ana V.;Liwo, Adam;Scheraga, Harold A.
通讯作者：
Scheraga, Harold A.
影响因子：
56.9
作者：
Shaw, David E.;Maragakis, Paul;Wriggers, Willy
通讯作者：
Wriggers, Willy
影响因子：
5.6
作者：
Jones, DT
通讯作者：
Jones, DT
影响因子：
3.4
作者：
Rhee, YM;Pande, VS
通讯作者：
Pande, VS