Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms. - Elodie Laine; Isaure Chauvot de Beauchêne; David Perahia; Christian Auclair; Luba Tchertanov (PLoS Comput. Biol., 2011)

GANM: A protein-ligand docking approach based on genetic algorithm and normal modes. - Angélica Nakagawa Lima; Eric Allison Philot; David Perahia; Antonio Sérgio Kimus Braz; Luis P. B. Scott (Appl. Math. Comput., 2012)

Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters. - Nohad Gresh; Krystel El Hage; David Perahia; Jean-Philip Piquemal; Catherine Berthomieu; Dorothée Berthomieu (J. Comput. Chem., 2014)

Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown. - Nohad Gresh; David Perahia; Benoit de Courcy; Johanna Foret; Celine Roux; Lea El-Khoury; Jean-Philip Piquemal; Laurent Salmon (J. Comput. Chem., 2016)

A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit). - Mauricio G. S. Costa; Charline Fagnen; Catherine Vénien-Bryan; David Perahia (J. Chem. Inf. Model., 2020)

Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules - Preliminary validations of a polarizable potential by ab initio quantum chemistry. - Nohad Gresh; David Perahia (J. Comput. Chem., 2021)

MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search. - Zakaria L. Dahmani; Ana Ligia Scott; Catherine Vénien-Bryan; David Perahia; Mauricio G. S. Costa (J. Chem. Inf. Model., 2024)