Both absolute and relative binding free energy calculations are an important technique for obtaining thermodynamic predictions in drug discovery, ligand and peptide binding prediction, and solvation free energies. The major methods are based on the free energy perturbation, thermodynamic integration, and lambda dynamics, which have different advantages and disadvantages in terms of calculation speed and accuracy. These methods are implemented in different simulation programs, so that preparations of initial modeling and necessary input files are quite different and challenging for most users. Moreover, preparations of systems containing combinatorial ligand structures are nontrivial, error-prone, and time consuming due to the alchemical hybridization of topologies and structures among the various derivatives. Here, I will talk about <i>CHARMM-GUI (Absolute / Relative) Ligand Binder </i>to help users to prepare absolute and relative free energy calculations by providing necessary input files and force field parameters for various simulation programs and free energy calculation methods. <br/>

CHARMM-GUI ligand binder for relative and absolute binding free energy calculations

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

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