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Coarse-grained potential for hydrogen bond interactions

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dc.abstract.enUnderstanding protein structure and dynamics is crucial for investigating numerous biological processes. This however requires proper description of molecular interactions, most notably hydrogen bonds, which are the driving force behind the folding of protein sequences into working molecules. Due to the multi-body character of this interaction, proper mathematical formulation has been a matter of long debate in the literature. This description becomes even more complex in reduced protein models. In this contribution, we propose a novel hydrogen bond energy function definition that is based only on Cα positions and used for coarse-grained simulations. We show that this new method has the capability to recognize hydrogen bonds with over 80% accuracy and can successfully identify β-sheet in β-amyloid peptide simulations.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorGront, Dominik
dc.contributor.authorKryś, Justyna
dc.date.accessioned2024-01-24T19:30:47Z
dc.date.available2024-01-24T19:30:47Z
dc.date.issued2023
dc.description.financeNie dotyczy
dc.description.volume124
dc.identifier.doi10.1016/J.JMGM.2023.108507
dc.identifier.issn1093-3263
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/103181
dc.identifier.weblinkhttps://api.elsevier.com/content/article/PII:S1093326323001055?httpAccept=text/xml
dc.languageeng
dc.pbn.affiliationchemical sciences
dc.relation.ispartofJournal of Molecular Graphics and Modelling
dc.relation.pages108507
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.subject.enCoarse grain methods
dc.subject.enHydrogen bond
dc.subject.enMean field force filed
dc.subject.enProtein modeling
dc.titleCoarse-grained potential for hydrogen bond interactions
dc.typeJournalArticle
dspace.entity.typePublication