ArticleJournal of biomolecular NMR2011
Biomolecular structure refinement using the GROMOS simulation software.
Article in Journal of biomolecular NMR, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Fluctuating β-Sheet Secondary Structure in DS119 Explains the Small Effects of Backbone N-Amination on Thermal Stability.Journal of peptide science : an official publication of the European Peptide Society · 2026Article
- Use of Measured Residual Dipolar Couplings to Calculate Residual Dipolar Couplings for a Protein Structure: A Case Study Using Hen Egg-White Lysozyme.Journal of chemical information and modeling · 2025Article
- Punica granatum leaf extract as a natural antibacterial agent explored by experimental and computational methods.Scientific reports · 2025Article
- Molecular Structure Refinement of a ß-Heptapeptide Based on Residual Dipolar Couplings: The Challenge of Extracting Structural Information from Measured RDCs.The journal of physical chemistry. B · 2025Article
- Stabilization of a miniprotein fold by an unpuckered proline surrogate.Communications chemistry · 2025Article
- Backbone N-Amination Promotes the Folding of β-Hairpin Peptides via a Network of Hydrogen Bonds.Journal of chemical information and modeling · 2022Article
- Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme.European biophysics journal : EBJ · 2022Article
- On the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study Using Hen Lysozyme.Chembiochem : a European journal of chemical biology · 2021Article
- On the use ofJournal of biomolecular NMR · 2021Article
- Molecular Conformations of Di-, Tri-, and Tetra-International journal of molecular sciences · 2019Article
- Genome-wide association study reveals a QTL and strong candidate genes for umbilical hernia in pigs on SSC14.BMC genomics · 2018Article
- On the use of time-averaging restraints when deriving biomolecular structure from ³Journal of biomolecular NMR · 2016Article
- Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations.European biophysics journal : EBJ · 2015Article
- Fitting alignment tensor components to experimental RDCs, CSAs and RQCs.Journal of biomolecular NMR · 2015Article
- Time-averaged order parameter restraints in molecular dynamics simulations.Journal of biomolecular NMR · 2014Article
- On the use of one-step perturbation to investigate the dependence of NOE-derived atom-atom distance bound violations of peptides upon a variation of force-field parameters.European biophysics journal : EBJ · 2014Article
- Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data.Journal of biomolecular NMR · 2013Article
- Multiple binding modes for palmitate to barley lipid transfer protein facilitated by the presence of proline 12.Protein science : a publication of the Protein Society · 2013Article
- On the calculation of ³Jαβ-coupling constants for side chains in proteins.Journal of biomolecular NMR · 2012Article
- An improved structural characterisation of reduced French bean plastocyanin based on NMR data and local-elevation molecular dynamics simulation.European biophysics journal : EBJ · 2012Article
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6 authors.
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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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.