FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2029564559> ?p ?o ?g. }

• W2029564559 endingPage "6594" @default.
• W2029564559 startingPage "6582" @default.
• W2029564559 abstract "In this work we demonstrate the use of a rigorous formalism for the extraction of state-to-state transition functions as a way to study the kinetics of protein folding in the context of a Markov chain. The approach is illustrated by its application to two different systems: a blocked alanine dipeptide in a vacuum and the C-terminal β-hairpin motif from protein G in water. The first system displays some of the desired features of the approach, whereas the second illustrates some of the challenges that must be overcome to apply the method to more complex biomolecular systems. For both example systems, Boltzmann weighted conformations produced by a replica exchange Monte Carlo procedure were used as starting states for kinetic trajectories. The alanine dipeptide displays Markovian behavior in a state space defined with respect to φ−ψ torsion angles. In contrast, Markovian behavior was not observed for the β-hairpin in a state space where all possible native hydrogen bonding patterns were resolved. This may be due to our choice of state definitions or sampling limitations. Furthermore, the use of different criteria for hydrogen bonding results in the apparent observation of different mechanisms from the same underlying data: one set of criteria indicate a zipping type of process, but another indicates more of a collapse followed by almost simultaneous formation of a large number of contacts. Analysis of long-lived states observed during the simulations of the β-hairpin suggests that important aspects of the folding process that are not captured by order parameters in common use include the formation of non-native hydrogen bonds and the degree and nature of salt bridge formation." @default.
• W2029564559 created "2016-06-24" @default.
• W2029564559 creator A5008933514 @default.
• W2029564559 creator A5012484892 @default.
• W2029564559 creator A5027317556 @default.
• W2029564559 creator A5037291190 @default.
• W2029564559 creator A5041944862 @default.
• W2029564559 creator A5047493562 @default.
• W2029564559 creator A5057623636 @default.
• W2029564559 creator A5058526411 @default.
• W2029564559 creator A5063152549 @default.
• W2029564559 creator A5078014032 @default.
• W2029564559 creator A5078270488 @default.
• W2029564559 date "2004-04-21" @default.
• W2029564559 modified "2023-10-10" @default.
• W2029564559 title "Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 2. Example Applications to Alanine Dipeptide and a β-Hairpin Peptide" @default.
• W2029564559 cites W1658649599 @default.
• W2029564559 cites W1898130445 @default.
• W2029564559 cites W1960408443 @default.
• W2029564559 cites W1966712500 @default.
• W2029564559 cites W1977482735 @default.
• W2029564559 cites W1997877357 @default.
• W2029564559 cites W1999521416 @default.
• W2029564559 cites W2008708467 @default.
• W2029564559 cites W2010631370 @default.
• W2029564559 cites W2018312454 @default.
• W2029564559 cites W2020346881 @default.
• W2029564559 cites W2023548777 @default.
• W2029564559 cites W2027854802 @default.
• W2029564559 cites W2035266068 @default.
• W2029564559 cites W2037410278 @default.
• W2029564559 cites W2043224212 @default.
• W2029564559 cites W2047510784 @default.
• W2029564559 cites W2051381895 @default.
• W2029564559 cites W2066010782 @default.
• W2029564559 cites W2067174909 @default.
• W2029564559 cites W2074684502 @default.
• W2029564559 cites W2078395305 @default.
• W2029564559 cites W2080131977 @default.
• W2029564559 cites W2085908066 @default.
• W2029564559 cites W2087356905 @default.
• W2029564559 cites W2089258285 @default.
• W2029564559 cites W2092853463 @default.
• W2029564559 cites W2095911937 @default.
• W2029564559 cites W2096649990 @default.
• W2029564559 cites W2101247857 @default.
• W2029564559 cites W2104414143 @default.
• W2029564559 cites W2106140689 @default.
• W2029564559 cites W2111339528 @default.
• W2029564559 cites W2117285383 @default.
• W2029564559 cites W2122199548 @default.
• W2029564559 cites W2122220546 @default.
• W2029564559 cites W2130390906 @default.
• W2029564559 cites W2131025577 @default.
• W2029564559 cites W2137841361 @default.
• W2029564559 cites W2146462263 @default.
• W2029564559 cites W2952680488 @default.
• W2029564559 cites W3104163644 @default.
• W2029564559 cites W4233269677 @default.
• W2029564559 doi "https://doi.org/10.1021/jp037422q" @default.
• W2029564559 hasPublicationYear "2004" @default.
• W2029564559 type Work @default.
• W2029564559 sameAs 2029564559 @default.
• W2029564559 citedByCount "162" @default.
• W2029564559 countsByYear W20295645592012 @default.
• W2029564559 countsByYear W20295645592013 @default.
• W2029564559 countsByYear W20295645592014 @default.
• W2029564559 countsByYear W20295645592015 @default.
• W2029564559 countsByYear W20295645592016 @default.
• W2029564559 countsByYear W20295645592017 @default.
• W2029564559 countsByYear W20295645592018 @default.
• W2029564559 countsByYear W20295645592019 @default.
• W2029564559 countsByYear W20295645592020 @default.
• W2029564559 countsByYear W20295645592021 @default.
• W2029564559 countsByYear W20295645592022 @default.
• W2029564559 countsByYear W20295645592023 @default.
• W2029564559 crossrefType "journal-article" @default.
• W2029564559 hasAuthorship W2029564559A5008933514 @default.
• W2029564559 hasAuthorship W2029564559A5012484892 @default.
• W2029564559 hasAuthorship W2029564559A5027317556 @default.
• W2029564559 hasAuthorship W2029564559A5037291190 @default.
• W2029564559 hasAuthorship W2029564559A5041944862 @default.
• W2029564559 hasAuthorship W2029564559A5047493562 @default.
• W2029564559 hasAuthorship W2029564559A5057623636 @default.
• W2029564559 hasAuthorship W2029564559A5058526411 @default.
• W2029564559 hasAuthorship W2029564559A5063152549 @default.
• W2029564559 hasAuthorship W2029564559A5078014032 @default.
• W2029564559 hasAuthorship W2029564559A5078270488 @default.
• W2029564559 hasConcept C112887158 @default.
• W2029564559 hasConcept C119857082 @default.
• W2029564559 hasConcept C121332964 @default.
• W2029564559 hasConcept C121864883 @default.
• W2029564559 hasConcept C147597530 @default.
• W2029564559 hasConcept C159467904 @default.
• W2029564559 hasConcept C178790620 @default.
• W2029564559 hasConcept C185592680 @default.
• W2029564559 hasConcept C204328495 @default.
• W2029564559 hasConcept C2779138802 @default.

• next