Journal
JOURNAL OF BIOMOLECULAR NMR
Volume 51, Issue 3, Pages 265-281Publisher
SPRINGER
DOI: 10.1007/s10858-011-9534-0
Keywords
GROMOS; Structure refinement; Crystallography; NMR
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Funding
- National Center of Competence in Research (NCCR) in Structural Biology
- Swiss National Science Foundation [200020-121913]
- European Research Council [228076]
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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.
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