ArticleJournal of chemical information and modeling2021
Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS.
Article in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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Who cites it
7 citing papers in PubMed.
- 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
- Achieving Chemical Accuracy in Cyclodextrin Host-Guest Binding via Integrative Atomistic Modelling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Development of a New AMBER Force Field for Cysteine and Histidine Cadmium-Binding Proteins and Its Validation Through QM/MM MD Simulations.Journal of computational chemistry · 2025Article
- PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files.Journal of computational chemistry · 2025Article
- Flavones in pomelo peel resist fibril formation of human islet amyloid polypeptide.Chinese herbal medicines · 2025Article
- Molecular Modelling of Ionic Liquids: Situations When Charge Scaling Seems Insufficient.Molecules (Basel, Switzerland) · 2023Article
- Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers.Journal of chemical theory and computation · 2022Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe a step-by-step protocol for the computation of absolute dissociation free energy with GROMACS code and PLUMED library, which exploits a combination of advanced sampling techniques and nonequilibrium alchemical methodologies. The computational protocol has been automated through an open source Python middleware (HPC_Drug) which allows one to set up the GROMACS/PLUMED input files for execution on high performing computing facilities. The proposed protocol, by exploiting its inherent parallelism and the power of the GROMACS code on graphical processing units, has the potential to afford accurate and precise estimates of the dissociation constants in drug-receptor systems described at the atomistic level. The procedure has been applied to the calculation of the absolute dissociation free energy of PF-07321332, an oral antiviral proposed by Pfizer, with the main protease (3CL
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