FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2938161746> ?p ?o ?g. }

• W2938161746 endingPage "3409" @default.
• W2938161746 startingPage "3402" @default.
• W2938161746 abstract "The NAST force field is a popular tool for modeling RNA and is typical of low-resolution approaches. Unfortunately, some combinations of bond and dihedral angles can reach cliffs on the energy landscape which lead to numerical disasters. We describe changes to the formulation (NAST improved, NASTI) which smooth the dihedral energy term when neighboring angles become flat. We also improved the fit to experimental structures by replacing the harmonic term for the backbone angles with spline functions and using a more sophisticated approach to calculate energies for fragments that span both helix and loop regions. A newer, larger set of structures was used for the parametrization. The new formulation can be run for millions of steps without a thermostat, whereas NAST routinely suffers numerical catastrophes. Simulations with NASTI showed no decrease in the quality of the structures as reflected by slightly better GDT-TS scores and, in three of the five cases, marginally better RMSD values when compared to the crystal structures." @default.
• W2938161746 created "2019-04-25" @default.
• W2938161746 creator A5002244022 @default.
• W2938161746 creator A5045896253 @default.
• W2938161746 creator A5079232742 @default.
• W2938161746 date "2019-04-19" @default.
• W2938161746 modified "2023-09-27" @default.
• W2938161746 title "Improving the Numerical Stability of the NAST Force Field for RNA Simulations" @default.
• W2938161746 cites W142718297 @default.
• W2938161746 cites W1982023619 @default.
• W2938161746 cites W1982366717 @default.
• W2938161746 cites W1995808589 @default.
• W2938161746 cites W2013417534 @default.
• W2938161746 cites W2014997764 @default.
• W2938161746 cites W2016486508 @default.
• W2938161746 cites W2020546070 @default.
• W2938161746 cites W2025775122 @default.
• W2938161746 cites W2033534238 @default.
• W2938161746 cites W2037500442 @default.
• W2938161746 cites W2041640931 @default.
• W2938161746 cites W2054697783 @default.
• W2938161746 cites W2085764610 @default.
• W2938161746 cites W2091705944 @default.
• W2938161746 cites W2108688393 @default.
• W2938161746 cites W2120974004 @default.
• W2938161746 cites W2129669590 @default.
• W2938161746 cites W2130350435 @default.
• W2938161746 cites W2135300233 @default.
• W2938161746 cites W2139597938 @default.
• W2938161746 cites W2150800446 @default.
• W2938161746 cites W2151596277 @default.
• W2938161746 cites W2341963847 @default.
• W2938161746 cites W2342307854 @default.
• W2938161746 cites W2401358542 @default.
• W2938161746 cites W2413334978 @default.
• W2938161746 cites W2584434271 @default.
• W2938161746 cites W2949223833 @default.
• W2938161746 cites W3105719651 @default.
• W2938161746 cites W4241935390 @default.
• W2938161746 doi "https://doi.org/10.1021/acs.jctc.9b00089" @default.
• W2938161746 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/31002506" @default.
• W2938161746 hasPublicationYear "2019" @default.
• W2938161746 type Work @default.
• W2938161746 sameAs 2938161746 @default.
• W2938161746 citedByCount "0" @default.
• W2938161746 crossrefType "journal-article" @default.
• W2938161746 hasAuthorship W2938161746A5002244022 @default.
• W2938161746 hasAuthorship W2938161746A5045896253 @default.
• W2938161746 hasAuthorship W2938161746A5079232742 @default.
• W2938161746 hasConcept C10803110 @default.
• W2938161746 hasConcept C112887158 @default.
• W2938161746 hasConcept C112972136 @default.
• W2938161746 hasConcept C11413529 @default.
• W2938161746 hasConcept C119857082 @default.
• W2938161746 hasConcept C120665830 @default.
• W2938161746 hasConcept C121332964 @default.
• W2938161746 hasConcept C154945302 @default.
• W2938161746 hasConcept C187819001 @default.
• W2938161746 hasConcept C202887219 @default.
• W2938161746 hasConcept C32909587 @default.
• W2938161746 hasConcept C41008148 @default.
• W2938161746 hasConcept C62520636 @default.
• W2938161746 hasConcept C74902906 @default.
• W2938161746 hasConcept C89025888 @default.
• W2938161746 hasConcept C97355855 @default.
• W2938161746 hasConceptScore W2938161746C10803110 @default.
• W2938161746 hasConceptScore W2938161746C112887158 @default.
• W2938161746 hasConceptScore W2938161746C112972136 @default.
• W2938161746 hasConceptScore W2938161746C11413529 @default.
• W2938161746 hasConceptScore W2938161746C119857082 @default.
• W2938161746 hasConceptScore W2938161746C120665830 @default.
• W2938161746 hasConceptScore W2938161746C121332964 @default.
• W2938161746 hasConceptScore W2938161746C154945302 @default.
• W2938161746 hasConceptScore W2938161746C187819001 @default.
• W2938161746 hasConceptScore W2938161746C202887219 @default.
• W2938161746 hasConceptScore W2938161746C32909587 @default.
• W2938161746 hasConceptScore W2938161746C41008148 @default.
• W2938161746 hasConceptScore W2938161746C62520636 @default.
• W2938161746 hasConceptScore W2938161746C74902906 @default.
• W2938161746 hasConceptScore W2938161746C89025888 @default.
• W2938161746 hasConceptScore W2938161746C97355855 @default.
• W2938161746 hasIssue "5" @default.
• W2938161746 hasLocation W29381617461 @default.
• W2938161746 hasLocation W29381617462 @default.
• W2938161746 hasOpenAccess W2938161746 @default.
• W2938161746 hasPrimaryLocation W29381617461 @default.
• W2938161746 hasRelatedWork W1980989103 @default.
• W2938161746 hasRelatedWork W2012551556 @default.
• W2938161746 hasRelatedWork W2043193484 @default.
• W2938161746 hasRelatedWork W2054248273 @default.
• W2938161746 hasRelatedWork W2065662306 @default.
• W2938161746 hasRelatedWork W2070534047 @default.
• W2938161746 hasRelatedWork W2131751919 @default.
• W2938161746 hasRelatedWork W2222589778 @default.
• W2938161746 hasRelatedWork W2319735119 @default.
• W2938161746 hasRelatedWork W2938161746 @default.
• W2938161746 hasVolume "15" @default.
• W2938161746 isParatext "false" @default.

• next