Matches in SemOpenAlex for { <https://semopenalex.org/work/W4379375944> ?p ?o ?g. }
- W4379375944 abstract "We present a hybrid, multi-method, computational scheme for protein/ligand systems well suited to be used on modern and forthcoming massively parallel computing systems. The scheme relies on a multi-scale polarizable molecular modeling, approach to perform molecular dynamics simulations, and on an efficient Density Functional Theory (DFT) linear scaling method to post-process simulation snapshots. We use this scheme to investigate recent α-ketoamide inhibitors targeting the main protease of the SARS-CoV-2 virus. We assessed the reliability and the coherence of the hybrid scheme, in particular, by checking the ability of MM and DFT to reproduce results from high-end ab initio computations regarding such inhibitors. The DFT approach enables an a posteriori fragmentation of the system and an investigation into the strength of interaction among identified fragment pairs. We show the necessity of accounting for a large set of plausible protease/inhibitor conformations to generate reliable interaction data. Finally, we point out ways to further improve α-ketoamide inhibitors to more strongly interact with particular protease domains neighboring the active site." @default.
- W4379375944 created "2023-06-06" @default.
- W4379375944 creator A5014327912 @default.
- W4379375944 creator A5020975847 @default.
- W4379375944 creator A5031324373 @default.
- W4379375944 creator A5044207730 @default.
- W4379375944 creator A5045907415 @default.
- W4379375944 creator A5070843073 @default.
- W4379375944 date "2023-06-05" @default.
- W4379375944 modified "2023-10-05" @default.
- W4379375944 title "Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with <i>α</i>-ketoamide inhibitors" @default.
- W4379375944 cites W1031578623 @default.
- W4379375944 cites W1648909007 @default.
- W4379375944 cites W1978005976 @default.
- W4379375944 cites W1980826833 @default.
- W4379375944 cites W1981368803 @default.
- W4379375944 cites W1993077801 @default.
- W4379375944 cites W2008382162 @default.
- W4379375944 cites W2012679265 @default.
- W4379375944 cites W2018120102 @default.
- W4379375944 cites W2025229221 @default.
- W4379375944 cites W2037210960 @default.
- W4379375944 cites W2043602240 @default.
- W4379375944 cites W2044310219 @default.
- W4379375944 cites W2057687078 @default.
- W4379375944 cites W2063939409 @default.
- W4379375944 cites W2064798852 @default.
- W4379375944 cites W2072977764 @default.
- W4379375944 cites W2082301489 @default.
- W4379375944 cites W2091114929 @default.
- W4379375944 cites W2096747776 @default.
- W4379375944 cites W2125037348 @default.
- W4379375944 cites W2126918460 @default.
- W4379375944 cites W2131197116 @default.
- W4379375944 cites W2138305674 @default.
- W4379375944 cites W2161605421 @default.
- W4379375944 cites W2284201926 @default.
- W4379375944 cites W2516321997 @default.
- W4379375944 cites W2563252550 @default.
- W4379375944 cites W2592319450 @default.
- W4379375944 cites W2607390045 @default.
- W4379375944 cites W2729895185 @default.
- W4379375944 cites W2746700686 @default.
- W4379375944 cites W2765435674 @default.
- W4379375944 cites W2775561819 @default.
- W4379375944 cites W2803570481 @default.
- W4379375944 cites W2954680217 @default.
- W4379375944 cites W3003900291 @default.
- W4379375944 cites W3004751286 @default.
- W4379375944 cites W3005775246 @default.
- W4379375944 cites W3011491147 @default.
- W4379375944 cites W3011701533 @default.
- W4379375944 cites W3013223828 @default.
- W4379375944 cites W3013468691 @default.
- W4379375944 cites W3013626655 @default.
- W4379375944 cites W3015608194 @default.
- W4379375944 cites W3020196527 @default.
- W4379375944 cites W3020300207 @default.
- W4379375944 cites W3023464695 @default.
- W4379375944 cites W3023999991 @default.
- W4379375944 cites W3027378187 @default.
- W4379375944 cites W3032956014 @default.
- W4379375944 cites W3034880338 @default.
- W4379375944 cites W3037963889 @default.
- W4379375944 cites W3042613582 @default.
- W4379375944 cites W3043456568 @default.
- W4379375944 cites W3049550177 @default.
- W4379375944 cites W3087078168 @default.
- W4379375944 cites W3093152392 @default.
- W4379375944 cites W3101252836 @default.
- W4379375944 cites W3102090680 @default.
- W4379375944 cites W3105360998 @default.
- W4379375944 cites W3107015841 @default.
- W4379375944 cites W3107647937 @default.
- W4379375944 cites W3113053264 @default.
- W4379375944 cites W3115855045 @default.
- W4379375944 cites W3127215132 @default.
- W4379375944 cites W3128673971 @default.
- W4379375944 cites W3128735479 @default.
- W4379375944 cites W3135003478 @default.
- W4379375944 cites W3137172923 @default.
- W4379375944 cites W3138132283 @default.
- W4379375944 cites W3159536657 @default.
- W4379375944 cites W3173261553 @default.
- W4379375944 cites W3176005660 @default.
- W4379375944 cites W3186391158 @default.
- W4379375944 cites W3194112255 @default.
- W4379375944 cites W3198339740 @default.
- W4379375944 cites W3198913336 @default.
- W4379375944 cites W3199648492 @default.
- W4379375944 cites W3204478979 @default.
- W4379375944 cites W3210754646 @default.
- W4379375944 cites W3214648030 @default.
- W4379375944 cites W4200233171 @default.
- W4379375944 cites W4213005008 @default.
- W4379375944 cites W4213016296 @default.
- W4379375944 cites W4220740715 @default.
- W4379375944 cites W4225786175 @default.
- W4379375944 cites W4234423475 @default.
- W4379375944 cites W4282916790 @default.