The Journal of Physical Chemistry B · 2020 · 140 citations · 39 references
Life SciencesInfectious DiseasesMolecular BiologyMolecular VirologyStructural BiologyVirologyAntiviral TherapyMolecular DynamicsNucleic Acid ModelingRna Polymerase StructureViral StructureVirus StructureBinding Free EnergyFree Energy PerturbationMechanism-based InhibitionSars-cov-2 Antiviral TherapyStructural VirologyViral Polymerase InhibitorsViral PolymerasesViral Rna Structure
from remdesivir over ATP indicates an effective replacement of ATP in blocking of the RdRp preinsertion site. Key residues D618, S549, and R555 are found to be the contributors to the binding affinity of remdesivir. These findings suggest that remdesivir can potentially act as a SARS-CoV-2 RNA-chain terminator, effectively stopping its RNA replication, with key residues also identified for future lead optimization and/or drug resistance studies.
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Scalable molecular dynamics with NAMD
J. C. Phillips, Rosemary Braun, Wei Wang et al. · Journal of Computational Chemistry · 2005 · 17.4K citations · Full text
Alessandro Laio, Michele Parrinello · Proceedings of the National Academy of Sciences · 2002 · 5.7K citations · Full text
Natural Sciences, Chemistry, Physics +17
Replica-exchange molecular dynamics method for protein folding
Yuji Sugita, Yuko Okamoto · Chemical Physics Letters · 1999 · 4.6K citations