FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2106560147> ?p ?o ?g. }

• W2106560147 abstract "All-atom force fields are now routinely used for more detailed understanding of protein folding mechanisms. However, it has been pointed out that use of all-atom force fields does not guarantee more accurate representations of proteins; in fact, sometimes it even leads to biased structural distributions. Indeed, several issues remain to be solved in force field developments, such as accurate treatment of implicit solvation for efficient conformational sampling and proper treatment of backbone interactions for secondary structure propensities. In this study, we first investigate the quality of several recently improved backbone interaction schemes in AMBER for folding simulations of a beta-hairpin peptide, and further study their influences on the peptide's folding mechanism. Due to the significant number of simulations needed for a thorough analysis of tested force fields, the implicit Poisson-Boltzmann solvent was used in all simulations. The chosen implicit solvent was found to be reasonable for studies of secondary structures based on a set of simulations of both alpha-helical and beta-hairpin peptides with the TIP3P explicit solvent as benchmark. Replica exchange molecular dynamics was also utilized for further efficient conformational sampling. Among the tested AMBER force fields, ff03 and a revised ff99 force field were found to produce structural and thermodynamic data in comparably good agreement with the experiment. However, detailed folding pathways, such as the order of backbone hydrogen bond zipping and the existence of intermediate states, are different between the two force fields, leading to force field-dependent folding mechanisms." @default.
• W2106560147 created "2016-06-24" @default.
• W2106560147 creator A5032088629 @default.
• W2106560147 creator A5083287504 @default.
• W2106560147 date "2006-11-01" @default.
• W2106560147 modified "2023-10-16" @default.
• W2106560147 title "Force field influences in β-hairpin folding simulations" @default.
• W2106560147 cites W1658649599 @default.
• W2106560147 cites W1960408443 @default.
• W2106560147 cites W1973060079 @default.
• W2106560147 cites W1976161355 @default.
• W2106560147 cites W1976499671 @default.
• W2106560147 cites W1979716756 @default.
• W2106560147 cites W2019723230 @default.
• W2106560147 cites W2028031397 @default.
• W2106560147 cites W2031273789 @default.
• W2106560147 cites W2035266068 @default.
• W2106560147 cites W2040809566 @default.
• W2106560147 cites W2042490093 @default.
• W2106560147 cites W2043182822 @default.
• W2106560147 cites W2044858517 @default.
• W2106560147 cites W2047510784 @default.
• W2106560147 cites W2048740445 @default.
• W2106560147 cites W2050333027 @default.
• W2106560147 cites W2056760934 @default.
• W2106560147 cites W2060447195 @default.
• W2106560147 cites W2064709968 @default.
• W2106560147 cites W2066010782 @default.
• W2106560147 cites W2067174909 @default.
• W2106560147 cites W2068800353 @default.
• W2106560147 cites W2069123478 @default.
• W2106560147 cites W2083232514 @default.
• W2106560147 cites W2087356905 @default.
• W2106560147 cites W2089258285 @default.
• W2106560147 cites W2095911937 @default.
• W2106560147 cites W2101247857 @default.
• W2106560147 cites W2104414143 @default.
• W2106560147 cites W2122199548 @default.
• W2106560147 cites W2122220546 @default.
• W2106560147 cites W2129071110 @default.
• W2106560147 cites W2131288855 @default.
• W2106560147 cites W2135469866 @default.
• W2106560147 cites W2140340353 @default.
• W2106560147 cites W2155524113 @default.
• W2106560147 cites W2155714626 @default.
• W2106560147 cites W2165222310 @default.
• W2106560147 doi "https://doi.org/10.1110/ps.062438006" @default.
• W2106560147 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2242415" @default.
• W2106560147 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/17075138" @default.
• W2106560147 hasPublicationYear "2006" @default.
• W2106560147 type Work @default.
• W2106560147 sameAs 2106560147 @default.
• W2106560147 citedByCount "60" @default.
• W2106560147 countsByYear W21065601472012 @default.
• W2106560147 countsByYear W21065601472013 @default.
• W2106560147 countsByYear W21065601472014 @default.
• W2106560147 countsByYear W21065601472015 @default.
• W2106560147 countsByYear W21065601472016 @default.
• W2106560147 countsByYear W21065601472017 @default.
• W2106560147 countsByYear W21065601472018 @default.
• W2106560147 countsByYear W21065601472019 @default.
• W2106560147 countsByYear W21065601472023 @default.
• W2106560147 crossrefType "journal-article" @default.
• W2106560147 hasAuthorship W2106560147A5032088629 @default.
• W2106560147 hasAuthorship W2106560147A5083287504 @default.
• W2106560147 hasBestOaLocation W21065601472 @default.
• W2106560147 hasConcept C10803110 @default.
• W2106560147 hasConcept C119599485 @default.
• W2106560147 hasConcept C121332964 @default.
• W2106560147 hasConcept C121864883 @default.
• W2106560147 hasConcept C127413603 @default.
• W2106560147 hasConcept C128747166 @default.
• W2106560147 hasConcept C147597530 @default.
• W2106560147 hasConcept C148093993 @default.
• W2106560147 hasConcept C159467904 @default.
• W2106560147 hasConcept C178790620 @default.
• W2106560147 hasConcept C185592680 @default.
• W2106560147 hasConcept C204328495 @default.
• W2106560147 hasConcept C2776545253 @default.
• W2106560147 hasConcept C32909587 @default.
• W2106560147 hasConcept C55493867 @default.
• W2106560147 hasConcept C59593255 @default.
• W2106560147 hasConcept C62520636 @default.
• W2106560147 hasConcept C64147673 @default.
• W2106560147 hasConceptScore W2106560147C10803110 @default.
• W2106560147 hasConceptScore W2106560147C119599485 @default.
• W2106560147 hasConceptScore W2106560147C121332964 @default.
• W2106560147 hasConceptScore W2106560147C121864883 @default.
• W2106560147 hasConceptScore W2106560147C127413603 @default.
• W2106560147 hasConceptScore W2106560147C128747166 @default.
• W2106560147 hasConceptScore W2106560147C147597530 @default.
• W2106560147 hasConceptScore W2106560147C148093993 @default.
• W2106560147 hasConceptScore W2106560147C159467904 @default.
• W2106560147 hasConceptScore W2106560147C178790620 @default.
• W2106560147 hasConceptScore W2106560147C185592680 @default.
• W2106560147 hasConceptScore W2106560147C204328495 @default.
• W2106560147 hasConceptScore W2106560147C2776545253 @default.
• W2106560147 hasConceptScore W2106560147C32909587 @default.
• W2106560147 hasConceptScore W2106560147C55493867 @default.
• W2106560147 hasConceptScore W2106560147C59593255 @default.

• next