FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2004516303> ?p ?o ?g. }

• W2004516303 endingPage "1772" @default.
• W2004516303 startingPage "1758" @default.
• W2004516303 abstract "Despite the many biological functions of RNA, very few drugs have been designed or found to target RNA. Here we report the results of molecular dynamics (MD) simulations and binding energy analyses on hepatitis C virus internal ribosome entry site (IRES) RNA in complex with highly charged 2-aminobenzimidazole inhibitors. Initial coordinates were taken from NMR and crystallography studies that had yielded different binding modes. During MD simulations, the RNA-inhibitor complex is stable in the crystal conformation but not in the NMR conformation. Additionally, we found that existing and standard MD trajectory postprocessing free energy methods, such as the MM-GBSA and MM-PBSA approaches available in AMBER, seem unsuitable to properly rank the binding energies of complexes between highly charged molecules. A better correlation with the experimental data was found using a rather simple binding enthalpy calculation based on the explicitly solvated potential energies. In anticipation of further growth in the use of small molecules to target RNA, we include results addressing the impact of charge assignment on docking, the structural role of magnesium in the IRES-inhibitor complex, the entropic contribution to binding energy, and simulations of a plausible scaffold design for new inhibitors." @default.
• W2004516303 created "2016-06-24" @default.
• W2004516303 creator A5011259040 @default.
• W2004516303 creator A5020579549 @default.
• W2004516303 creator A5034998740 @default.
• W2004516303 creator A5073848973 @default.
• W2004516303 date "2014-06-03" @default.
• W2004516303 modified "2023-10-14" @default.
• W2004516303 title "Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations" @default.
• W2004516303 cites W1722753864 @default.
• W2004516303 cites W1971820073 @default.
• W2004516303 cites W1976161355 @default.
• W2004516303 cites W1976499671 @default.
• W2004516303 cites W1978330227 @default.
• W2004516303 cites W1981225934 @default.
• W2004516303 cites W1984902027 @default.
• W2004516303 cites W1985133799 @default.
• W2004516303 cites W1985371388 @default.
• W2004516303 cites W1988613101 @default.
• W2004516303 cites W1991667171 @default.
• W2004516303 cites W1994861731 @default.
• W2004516303 cites W1998643862 @default.
• W2004516303 cites W2000613080 @default.
• W2004516303 cites W2001368737 @default.
• W2004516303 cites W2014118668 @default.
• W2004516303 cites W2015688756 @default.
• W2004516303 cites W2017019577 @default.
• W2004516303 cites W2017829285 @default.
• W2004516303 cites W2019943197 @default.
• W2004516303 cites W2022885475 @default.
• W2004516303 cites W2026945988 @default.
• W2004516303 cites W2029863180 @default.
• W2004516303 cites W2030574185 @default.
• W2004516303 cites W2035687084 @default.
• W2004516303 cites W2036011280 @default.
• W2004516303 cites W2037535298 @default.
• W2004516303 cites W2040895520 @default.
• W2004516303 cites W2042855904 @default.
• W2004516303 cites W2048962220 @default.
• W2004516303 cites W2052518379 @default.
• W2004516303 cites W2053858804 @default.
• W2004516303 cites W2057130873 @default.
• W2004516303 cites W2058052041 @default.
• W2004516303 cites W2063292547 @default.
• W2004516303 cites W2064293171 @default.
• W2004516303 cites W2072660673 @default.
• W2004516303 cites W2072683434 @default.
• W2004516303 cites W2074538084 @default.
• W2004516303 cites W2081046982 @default.
• W2004516303 cites W2081311256 @default.
• W2004516303 cites W2085726941 @default.
• W2004516303 cites W2085954575 @default.
• W2004516303 cites W2092500668 @default.
• W2004516303 cites W2093140638 @default.
• W2004516303 cites W2093649670 @default.
• W2004516303 cites W2106140689 @default.
• W2004516303 cites W2110283222 @default.
• W2004516303 cites W2114135904 @default.
• W2004516303 cites W2118233996 @default.
• W2004516303 cites W2119102790 @default.
• W2004516303 cites W2132629607 @default.
• W2004516303 cites W2136729627 @default.
• W2004516303 cites W2139839673 @default.
• W2004516303 cites W2146783323 @default.
• W2004516303 cites W2147993766 @default.
• W2004516303 cites W2163915395 @default.
• W2004516303 cites W2324524889 @default.
• W2004516303 cites W4210406109 @default.
• W2004516303 cites W4236566602 @default.
• W2004516303 doi "https://doi.org/10.1021/ci500132c" @default.
• W2004516303 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4076022" @default.
• W2004516303 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/24835734" @default.
• W2004516303 hasPublicationYear "2014" @default.
• W2004516303 type Work @default.
• W2004516303 sameAs 2004516303 @default.
• W2004516303 citedByCount "12" @default.
• W2004516303 countsByYear W20045163032015 @default.
• W2004516303 countsByYear W20045163032016 @default.
• W2004516303 countsByYear W20045163032017 @default.
• W2004516303 countsByYear W20045163032018 @default.
• W2004516303 countsByYear W20045163032019 @default.
• W2004516303 countsByYear W20045163032021 @default.
• W2004516303 countsByYear W20045163032022 @default.
• W2004516303 countsByYear W20045163032023 @default.
• W2004516303 crossrefType "journal-article" @default.
• W2004516303 hasAuthorship W2004516303A5011259040 @default.
• W2004516303 hasAuthorship W2004516303A5020579549 @default.
• W2004516303 hasAuthorship W2004516303A5034998740 @default.
• W2004516303 hasAuthorship W2004516303A5073848973 @default.
• W2004516303 hasBestOaLocation W20045163031 @default.
• W2004516303 hasConcept C104317684 @default.
• W2004516303 hasConcept C12554922 @default.
• W2004516303 hasConcept C147597530 @default.
• W2004516303 hasConcept C159110408 @default.
• W2004516303 hasConcept C185592680 @default.
• W2004516303 hasConcept C41685203 @default.
• W2004516303 hasConcept C55493867 @default.
• W2004516303 hasConcept C59593255 @default.

• next