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Cited by 19Computational Drug Discovery MethodsProtein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

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QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

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Ojha, Anupam Anand, Votapka, Lane William, Amaro, Rommie Elizabeth·2023·Chemical Science
DOI 10.1039/d3sc04195fPMC PMC10664576

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Abstract

Graphical representation of the partition of the phase-space of the receptor (grey)-ligand (yellow) complex into the MD region (further partitioned into Voronoi cells) and the BD region.

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Metadata

Authors
Ojha, A. A., Votapka, L. W., & Amaro, R. E.
Affiliations
University of California San Diego (US)
Corresponding author
Amaro, Rommie Elizabeth
ORCID
Venue
Chemical Science
Publisher
Royal Society of Chemistry (RSC)
Published
2023
Volume
14
Issue
45
Pages
13159-13175
ISSN
  • 2041-6520 (ISSN-L)
  • 2041-6539
DOI
10.1039/d3sc04195f
PMC
PMC10664576
OpenAlex
W4387918243
Cited by
19
References
5
Citations by year
2026: 6 · 2025: 6 · 2024: 6 · 2023: 1
FWCI
2.71
Type
journal article
Language
en
Open access
Licence
Locations
  • Chemical Science (publishedVersion, cc-by-nc)
  • ChemRxiv (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc)
Funders
National Science Foundation (OAC-1547580, CHE060063, NIH GM132826)
Topics
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
Keywords
ligand binding sites, molecular dynamics, Voronoi cells, phase space partitioning, binding free energy, receptor-ligand complex

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