Abstract
The calculations of the free energy of ligand binding with a receptor (most often, protein) are widely used in the rational design of new bioactive compounds. The gold standard of such calculations is the equilibrium methods based on molecular dynamics and the “alchemical” transformations, including the thermodynamic integration and Bennett method. Technically, these methods call for introduction of additional restraints on the mutual arrangement of atoms in the ligand–receptor system. A plugin to the PyMOL molecular graphics system has been developed to facilitate the introduction of required restraints and analytical calculation of correction when computing the free energy of ligand‒receptor (protein) binding.
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ACKNOWLEDGMENTS
The study was carried out using the equipment of the Shared Equipment Center of the Federal Research Center “Crystallography and Photonics” of the Russian Academy of Sciences.
Funding
This study was carried out within the state assignment to the Federal Research Center “Crystallography and Photonics” of the Russian Academy of Sciences and supported by the Ministry of Science and Higher Education of the Russian Federation, project no. RFMEFI62119X0035.
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Translated by E. Bondareva
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Lashkov, A.A., Tolmachev, I.V., Eistrikh-Heller, P.A. et al. PyFepRestr: Plugin to PyMOL Molecular Graphics System for Calculating the Free Energy of Ligand‒Receptor Binding. Crystallogr. Rep. 66, 861–865 (2021). https://doi.org/10.1134/S1063774521050126
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DOI: https://doi.org/10.1134/S1063774521050126