2006
Comparison of multiple Amber force fields and development of improved protein backbone parameters
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins Structure Function And Bioinformatics 2006, 65: 712-725. PMID: 16981200, PMCID: PMC4805110, DOI: 10.1002/prot.21123.Peer-Reviewed Original ResearchConceptsSecondary structure elementsConformational preferencesForce fieldExperimental NMR relaxation dataDihedral termsBackbone dihedralsAb initio quantum mechanical calculationsInitio quantum mechanical calculationsConformers of glycineAMBER force fieldQuantum mechanical calculationsFf99 force fieldAMBER simulation packageTested protein systemsAlpha-helicesAlanine tetrapeptideMechanical calculationsAlanine peptidesAmberBiomolecular simulationsBackbone parametersStructural elementsProtein systemsFf99Parameter settings
2002
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins
Okur A, Strockbine B, Hornak V, Simmerling C. Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. Journal Of Computational Chemistry 2002, 24: 21-31. PMID: 12483672, DOI: 10.1002/jcc.10184.Peer-Reviewed Original ResearchConceptsForce fieldMolecular mechanics force fieldMolecular mechanics parametersMechanics force fieldForce field transferabilityModified force fieldFf99 force fieldMolecular dynamics simulationsSmall model systemsMolecular dynamicsAMBER packageModel peptidesDynamics simulationsAlpha-helical conformationConformationFf99Beta-hairpinStructural dataStructural behaviorSample structureSmall peptidesFf94TransferExperimental dataModel system
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply