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Journal of Computer-Aided Molecular Design|October 9, 2021
On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challengePiero Procacci, Marina MacchiagodenaJournal of Molecular Graphics & Modelling|October 15, 2021
Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main proteaseMarina Macchiagodena, Marco Pagliai, Piero ProcacciChemical Physics Letters|April 22, 2020
Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modelingMarina Macchiagodena, Marco Pagliai, Piero ProcacciJournal 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 ProcacciChemmedchem|March 8, 2024
Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical SimulationsGiorgio Di Paco, Marina Macchiagodena, Piero ProcacciThe Journal of Physical Chemistry Letters|October 5, 2019
Evidence of a Low-High Density Turning Point in Liquid Water at Ordinary Temperature under Pressure: A Molecular Dynamics StudyMarco Pagliai, Marina Macchiagodena, Piero Procacci, et al.Journal of Chemical Information and Modeling|November 1, 2021
Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACSMarina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, et al.ACS Omega|July 9, 2020
Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-ProteinsMarina Macchiagodena, Marco Pagliai, Claudia Andreini, et al.Journal of Chemical Information and Modeling|August 7, 2019
Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein LigandsMarina Macchiagodena, Marco Pagliai, Claudia Andreini, et al.Chemical Communications (Cambridge, England)|July 8, 2020
Interaction of hydroxychloroquine with SARS-CoV2 functional proteins using all-atoms non-equilibrium alchemical simulationsPiero Procacci, Marina Macchiagodena, Marco Pagliai, et al.Pageof 10