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10.1002/cmdc.202100156

http://scihub22266oqcxt.onion/10.1002/cmdc.202100156
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33797868!8250706!33797868
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suck abstract from ncbi


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pmid33797868      ChemMedChem 2021 ; 16 (13): 2075-2081
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  • Inspecting the Mechanism of Fragment Hits Binding on SARS-CoV-2 M(pro) by Using Supervised Molecular Dynamics (SuMD) Simulations #MMPMID33797868
  • Bissaro M; Bolcato G; Pavan M; Bassani D; Sturlese M; Moro S
  • ChemMedChem 2021[Jul]; 16 (13): 2075-2081 PMID33797868show ga
  • Computational approaches supporting the early characterization of fragment molecular recognition mechanism represent a valuable complement to more expansive and low-throughput experimental techniques. In this retrospective study, we have investigated the geometric accuracy with which high-throughput supervised molecular dynamics simulations (HT-SuMD) can anticipate the experimental bound state for a set of 23 fragments targeting the SARS-CoV-2 main protease. Despite the encouraging results herein reported, in line with those previously described for other MD-based posing approaches, a high number of incorrect binding modes still complicate HT-SuMD routine application. To overcome this limitation, fragment pose stability has been investigated and integrated as part of our in-silico pipeline, allowing us to prioritize only the more reliable predictions.
  • |*Molecular Dynamics Simulation[MESH]
  • |Binding Sites[MESH]
  • |COVID-19/pathology/virology[MESH]
  • |Databases, Protein[MESH]
  • |Humans[MESH]
  • |Ligands[MESH]
  • |Protease Inhibitors/*chemistry/metabolism[MESH]
  • |Retrospective Studies[MESH]
  • |SARS-CoV-2/isolation & purification/*metabolism[MESH]


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