David Perahia

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 4

Top Topics

Expectation Maximization

Molecular Dynamics

Scientific Data

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

Publications

Zakaria L. Dahmani, Ana Ligia Scott, Catherine Vénien-Bryan, David Perahia, Mauricio G. S. Costa
MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search. J. Chem. Inf. Model. 64 (13) (2024)
Nohad Gresh, David Perahia
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. J. Comput. Chem. 42 (20) (2021)
Mauricio G. S. Costa, Charline Fagnen, Catherine Vénien-Bryan, David Perahia
A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit). J. Chem. Inf. Model. 60 (5) (2020)
Nohad Gresh, David Perahia, Benoit de Courcy, Johanna Foret, Celine Roux, Lea El-Khoury, Jean-Philip Piquemal, Laurent Salmon
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. J. Comput. Chem. 37 (32) (2016)
Nohad Gresh, Krystel El Hage, David Perahia, Jean-Philip Piquemal, Catherine Berthomieu, Dorothée Berthomieu
Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: Bimetallic binding site and structured waters. J. Comput. Chem. 35 (29) (2014)
Angélica Nakagawa Lima, Eric Allison Philot, David Perahia, Antonio Sérgio Kimus Braz, Luis P. B. Scott
GANM: A protein-ligand docking approach based on genetic algorithm and normal modes. Appl. Math. Comput. 219 (2) (2012)
Elodie Laine, Isaure Chauvot de Beauchêne, David Perahia, Christian Auclair, Luba Tchertanov
Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms. PLoS Comput. Biol. 7 (6) (2011)