{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Stroet M"],"funding":["Bundesministerium f?r Digitalisierung und Wirtschaftsstandort","Christian Doppler Forschungsgesellschaft","?sterreichische Nationalstiftung f?r Forschung, Technologie und Entwicklung","Australian Research Data Commons","Australian Research Council"],"pagination":["4602-4620"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11103706"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["128(19)"],"pubmed_abstract":["Molecular dynamics simulations depend critically on the quality of the force field used to describe the interatomic interactions and the extent to which it has been validated for use in a specific application. Using a curated test set of 52 high-resolution structures, 39 derived from X-ray diffraction and 13 solved using NMR, we consider the extent to which different parameter sets of the GROMOS protein force field can be distinguished based on comparing a range of structural criteria, including the number of backbone hydrogen bonds, the number of native hydrogen bonds, polar and nonpolar solvent-accessible surface area, radius of gyration, the prevalence of secondary structure elements, <i>J</i>-coupling constants, nuclear Overhauser effect (NOE) intensities, positional root-mean-square d"],"journal":["The journal of physical chemistry. B"],"pubmed_title":["On the Validation of Protein Force Fields Based on Structural Criteria."],"pmcid":["PMC11103706"],"funding_grant_id":["DP150101097","DP723","DP180101421"],"pubmed_authors":["Malde AK","Stroet M","van den Bergen G","Mark AE","Sykacek P","Setz M","Lee T","Oostenbrink C"],"additional_accession":[]},"is_claimable":false,"name":"On the Validation of Protein Force Fields Based on Structural Criteria.","description":"Molecular dynamics simulations depend critically on the quality of the force field used to describe the interatomic interactions and the extent to which it has been validated for use in a specific application. Using a curated test set of 52 high-resolution structures, 39 derived from X-ray diffraction and 13 solved using NMR, we consider the extent to which different parameter sets of the GROMOS protein force field can be distinguished based on comparing a range of structural criteria, including the number of backbone hydrogen bonds, the number of native hydrogen bonds, polar and nonpolar solvent-accessible surface area, radius of gyration, the prevalence of secondary structure elements, <i>J</i>-coupling constants, nuclear Overhauser effect (NOE) intensities, positional root-mean-square d","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 May","modification":"2026-06-02T10:28:23.352Z","creation":"2026-05-26T03:06:47.286Z"},"accession":"S-EPMC11103706","cross_references":{"pubmed":["38711373"],"doi":["10.1021/acs.jpcb.3c08469"]}}