title: Biomolecular structure refinement using the GROMOS simulation software.
abstract: 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.
authors.affiliation: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zürich, Switzerland.
authors.forename: Nathan
authors.initials: N
authors.lastname: Schmid
authors.forename: Jane R
authors.initials: JR
authors.lastname: Allison
authors.forename: Jožica
authors.initials: J
authors.lastname: Dolenc
authors.forename: Andreas P
authors.initials: AP
authors.lastname: Eichenberger
authors.forename: Anna-Pitschna E
authors.initials: AP
authors.lastname: Kunz
authors.forename: Wilfred F
authors.initials: WF
authors.lastname: van Gunsteren
mesh_terms: D003198:Computer Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software; D013816:Thermodynamics
chemical_list: D011506:Proteins