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Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS.
Macchiagodena, Marina; Karrenbrock, Maurice; Pagliai, Marco; Procacci, Piero.
  • Macchiagodena M; Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
  • Karrenbrock M; Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
  • Pagliai M; Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
  • Procacci P; Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
J Chem Inf Model ; 61(11): 5320-5326, 2021 11 22.
Article in English | MEDLINE | ID: covidwho-1493001
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 (3CLpro) of SARS-CoV-2.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Molecular Dynamics Simulation / COVID-19 Language: English Journal: J Chem Inf Model Journal subject: Medical Informatics / Chemistry Year: 2021 Document Type: Article Affiliation country: Acs.jcim.1c00909

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Molecular Dynamics Simulation / COVID-19 Language: English Journal: J Chem Inf Model Journal subject: Medical Informatics / Chemistry Year: 2021 Document Type: Article Affiliation country: Acs.jcim.1c00909