FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4309656719> ?p ?o ?g. }

• W4309656719 endingPage "10399" @default.
• W4309656719 startingPage "10384" @default.
• W4309656719 abstract "The profile of shapes presented by a cyclic peptide modulates its therapeutic efficacy and is represented by the ensemble of its sampled conformations. Although some algorithms excel at creating a diverse ensemble of cyclic peptide conformations, they seldom address the entropic contribution of flexible conformations and often have significant practical difficulty producing an ensemble with converged and reliable thermodynamic properties. In this study, an accelerated molecular dynamics (MD) method, namely, reservoir replica exchange MD (R-REMD or Res-REMD), was implemented in GROMACS ver. 4.6.7 and benchmarked on two small cyclic peptide model systems: a cyclized furin cleavage site of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (cyclo-(CGPRRARSG)) and oxytocin (disulfide-bonded CYIQNCPLG). Additionally, we also benchmarked Res-REMD on alanine dipeptide and Trpzip2 to demonstrate its validity and efficiency over REMD. For Trpzip2, Res-REMD coupled with an umbrella-sampling-derived reservoir generated similar folded fractions as regular REMD but on a much faster time scale. For cyclic peptides, Res-REMD appeared to be marginally faster than REMD in ensemble generation. Finally, Res-REMD was more effective in sampling rare events such as trans to cis peptide bond isomerization. We provide a GitHub page with the modified GROMACS source code for running Res-REMD at https://github.com/PlotkinLab/Reservoir-REMD." @default.
• W4309656719 created "2022-11-29" @default.
• W4309656719 creator A5017392485 @default.
• W4309656719 creator A5037783693 @default.
• W4309656719 creator A5091223520 @default.
• W4309656719 date "2022-11-21" @default.
• W4309656719 modified "2023-10-17" @default.
• W4309656719 title "Ensemble Generation for Linear and Cyclic Peptides Using a Reservoir Replica Exchange Molecular Dynamics Implementation in GROMACS" @default.
• W4309656719 cites W1510998615 @default.
• W4309656719 cites W1560481517 @default.
• W4309656719 cites W1583115566 @default.
• W4309656719 cites W1964839527 @default.
• W4309656719 cites W1965555277 @default.
• W4309656719 cites W1967671116 @default.
• W4309656719 cites W1968790827 @default.
• W4309656719 cites W1970900907 @default.
• W4309656719 cites W1971575413 @default.
• W4309656719 cites W1972013995 @default.
• W4309656719 cites W1974464394 @default.
• W4309656719 cites W1976499671 @default.
• W4309656719 cites W1977874258 @default.
• W4309656719 cites W1986986500 @default.
• W4309656719 cites W1990719397 @default.
• W4309656719 cites W1993321394 @default.
• W4309656719 cites W2000347480 @default.
• W4309656719 cites W2003728701 @default.
• W4309656719 cites W2004931090 @default.
• W4309656719 cites W2010386565 @default.
• W4309656719 cites W2011177250 @default.
• W4309656719 cites W2013145865 @default.
• W4309656719 cites W2015870840 @default.
• W4309656719 cites W2019218232 @default.
• W4309656719 cites W2023018411 @default.
• W4309656719 cites W2024726841 @default.
• W4309656719 cites W2024762727 @default.
• W4309656719 cites W2025157895 @default.
• W4309656719 cites W2026692111 @default.
• W4309656719 cites W2027255849 @default.
• W4309656719 cites W2029120587 @default.
• W4309656719 cites W2032363535 @default.
• W4309656719 cites W2033529815 @default.
• W4309656719 cites W2040809566 @default.
• W4309656719 cites W2041026060 @default.
• W4309656719 cites W2044882887 @default.
• W4309656719 cites W2044934618 @default.
• W4309656719 cites W2047730466 @default.
• W4309656719 cites W2048304660 @default.
• W4309656719 cites W2061543974 @default.
• W4309656719 cites W2065864578 @default.
• W4309656719 cites W2072261891 @default.
• W4309656719 cites W2078145018 @default.
• W4309656719 cites W2078374001 @default.
• W4309656719 cites W2085142174 @default.
• W4309656719 cites W2087774804 @default.
• W4309656719 cites W2090247295 @default.
• W4309656719 cites W2090806570 @default.
• W4309656719 cites W2094795801 @default.
• W4309656719 cites W2099111195 @default.
• W4309656719 cites W2103072162 @default.
• W4309656719 cites W2103723321 @default.
• W4309656719 cites W2104529244 @default.
• W4309656719 cites W2117285383 @default.
• W4309656719 cites W2119052082 @default.
• W4309656719 cites W2121529915 @default.
• W4309656719 cites W2130974803 @default.
• W4309656719 cites W2144562104 @default.
• W4309656719 cites W2146950091 @default.
• W4309656719 cites W2149442325 @default.
• W4309656719 cites W2158476854 @default.
• W4309656719 cites W2161447764 @default.
• W4309656719 cites W2161605421 @default.
• W4309656719 cites W2162581294 @default.
• W4309656719 cites W2167062204 @default.
• W4309656719 cites W2204230050 @default.
• W4309656719 cites W2226825552 @default.
• W4309656719 cites W2315297180 @default.
• W4309656719 cites W2327370752 @default.
• W4309656719 cites W2342488026 @default.
• W4309656719 cites W2346417861 @default.
• W4309656719 cites W2473618562 @default.
• W4309656719 cites W2484160537 @default.
• W4309656719 cites W2516147178 @default.
• W4309656719 cites W2520613901 @default.
• W4309656719 cites W2555870966 @default.
• W4309656719 cites W2559132852 @default.
• W4309656719 cites W2570104014 @default.
• W4309656719 cites W2594502287 @default.
• W4309656719 cites W2622272872 @default.
• W4309656719 cites W2739232261 @default.
• W4309656719 cites W2754199378 @default.
• W4309656719 cites W2773080986 @default.
• W4309656719 cites W2794605220 @default.
• W4309656719 cites W2796077280 @default.
• W4309656719 cites W2797220725 @default.
• W4309656719 cites W2885614068 @default.
• W4309656719 cites W2898459031 @default.
• W4309656719 cites W2900679761 @default.
• W4309656719 cites W2915491770 @default.

• next