Biomolecular structure refinement using the GROMOS simulation software

被引：44

作者：

Schmid, Nathan ^{[1
]}

Allison, Jane R. ^{[1
]}

Dolenc, Jozica ^{[1
,2
]}

Eichenberger, Andreas P. ^{[1
]}

Kunz, Anna-Pitschna E. ^{[1
]}

van Gunsteren, Wilfred F. ^{[1
]}

机构：

[1] ETH, Swiss Fed Inst Technol, Phys Chem Lab, CH-8093 Zurich, Switzerland

[2] Univ Ljubljana, Fac Chem & Chem Technol, Ljubljana 1000, Slovenia

来源：

JOURNAL OF BIOMOLECULAR NMR | 2011年 / 51卷 / 03期

基金：

欧洲研究理事会; 瑞士国家科学基金会;

关键词：

GROMOS; Structure refinement; Crystallography; NMR; MONTE-CARLO METHOD; MOLECULAR-DYNAMICS; FORCE-FIELD; LOCAL-ELEVATION; PROTEIN; CONSTRAINTS; RELAXATION; RESTRAINTS; DEPENDENCE; MOTION;

D O I：

10.1007/s10858-011-9534-0

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, (3) J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

引用

页码：265 / 281

页数：17

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