ArticleJournal of chemical theory and computation2020
Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 44 citations in OpenAlex.
- One Blob to Rule Them All: A Universal Dual-Topology Nonequilibrium Framework for Relative and Absolute Binding Free Energies via a Lennard-Jones Blob Reference.Journal of chemical theory and computation · 2026Article
- An efficient computational chemistry approach to generating negative data for drug discovery pipeline validation.Frontiers in bioinformatics · 2026Article
- PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files.Journal of computational chemistry · 2025Article
- Absolute Binding Free Energies with OneOPES.The journal of physical chemistry letters · 2024Article
- The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.Physical chemistry chemical physics : PCCP · 2024Article
- Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach.Journal of chemical theory and computation · 2022Article
- Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers.Journal of chemical theory and computation · 2022Article
- Haste makes waste: A critical review of docking-based virtual screening in drug repurposing for SARS-CoV-2 main protease (M-pro) inhibition.Medicinal research reviews · 2022Review
- Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease.Journal of molecular graphics & modelling · 2022Article
- Identifying the Hot Spot Residues of the SARS-CoV-2 Main Protease Using MM-PBSA and Multiple Force Fields.Life (Basel, Switzerland) · 2021Article
- Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS.Journal of chemical information and modeling · 2021Article
- On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge.Journal of computer-aided molecular design · 2021Article
- Potential inhibitors for SARS-CoV-2 Mpro from marine compounds.RSC advances · 2021Article
- Prioritisation of Compounds for 3CLMolecules (Basel, Switzerland) · 2021Article
- Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations.The journal of physical chemistry. B · 2021Article
- Article
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the context of drug-receptor binding affinity calculations using molecular dynamics techniques, we implemented a combination of Hamiltonian replica exchange (HREM) and a novel nonequilibrium alchemical methodology, called virtual double-system single-box, with increased accuracy, precision, and efficiency with respect to the standard nonequilibrium approaches. The method has been applied for the determination of absolute binding free energies of 16 newly designed noncovalent ligands of the main protease (3CL
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.