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Physical Chemistry Chemical Physics : PCCP|May 9, 2013
The conformational landscape of tartrate-based inhibitors of the TACE enzyme as revealed by Hamiltonian Replica Exchange simulationCarlo Guardiani, Piero ProcacciJournal of Computer-Aided Molecular Design|October 19, 2019
SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approachesPiero Procacci, Guido GuarnieriJournal of Chemical Theory and Computation|January 30, 2019
Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic MoleculesDario Vassetti, Marco Pagliai, Piero ProcacciChemical Physics Letters|April 22, 2020
Identification of potential binders of the main protease 3CL<sup>pro</sup> of the COVID-19 via structure-based ligand design and molecular modelingMarina Macchiagodena, Marco Pagliai, Piero ProcacciJournal of Computer-Aided Molecular Design|August 22, 2018
SAMPL6 host-guest blind predictions using a non equilibrium alchemical approachPiero Procacci, Massimiliano Guarrasi, Guido GuarnieriJournal of Computational Chemistry|January 27, 2023
NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemesMarina Macchiagodena, Marco Pagliai, Piero ProcacciJournal of Chemical Theory and Computation|November 19, 2015
Energy-Driven Undocking (EDU-HREM) in Solute Tempering Replica Exchange SimulationsPiero Procacci, Marco Bizzarri, Simone MarsiliPhysical Chemistry Chemical Physics : PCCP|May 20, 2016
II. Dissociation free energies in drug-receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligandsFrancesca Nerattini, Riccardo Chelli, Piero ProcacciPhysical Review. E, Statistical, Nonlinear, and Soft Matter Physics|June 4, 2008
Calculation of the potential of mean force from nonequilibrium measurements via maximum likelihood estimatorsRiccardo Chelli, Simone Marsili, Piero ProcacciThe Journal of Physical Chemistry. B|April 20, 2011
Intraligand hydrophobic interactions rationalize drug affinities for peptidyl-prolyl cis-trans isomerase proteinMarco Bizzarri, Simone Marsili, Piero ProcacciPageof 13