Modeling and simulation
Biospring is a molecular simulation software based on a spring network model, including non-bonded interactions, especially designed for Interactive Molecular Dynamics by Olivier Delalande, Nicolas Férey, Alex Tek, Benoist Laurent and Marc Baaden
The Collective Variables Module plugs into molecular dynamics simulation engines such as NAMD and LAMMPS or analysis tools such as VMD and provides flexible and powerful analysis and biasing on collective variables, including adaptive time-dependent biases. By Giacomo Fiorin (Temple University) and Jérôme Hénin.
Driving Molecular Dynamics codes by coupling with a CPU intensive visualization module by Olivier Delalande, Nicolas Férey, Gilles Grasseau and Marc Baaden.
A script allowing simulated tempering with on the fly scheme weight determination in explicit solvent with GROMACS by Tong Zhang, Phuong Nguyen and Philippe Derreumaux. [Download script]
This automatic tool will allow you to generate the OPEP files of your systems required to be used for ART, MD, REMS, ST, MUPHY, MD/DRIVER softwares based in the OPEP v3 and v4 potential. This automatic procedure was designed by Jean-François St-Pierre, Normand Mousseau and Philippe Derreumaux
A de novo peptide and miniprotein structure prediction server by Julien Maupetit, Philippe Derreumaux and Pierre Tuffery
Multi-Copy/Monte-Carlo : A Macromolecular Docking Program by Karine Bastard, Aurélien Thureau, Richard Lavery and Chantal Prevost
Macromolecular docking Py/C++ library for coarse grain or atomic representations of proteins and DNA, by Adrien Saladin, Pierre Poulain, Sébastien Fiorrucci, Martin Zacharias, Benoist Laurent, Charles H. Robert, Tap Ha Duong and Chantal Prévost
Visualization and analysis
Epock is a program designed to efficiently calculate binding pocket volumes along extensive sets of MD trajectories by Benoist Laurent, Mathieu Chavent, Tristan Cragnolini, Anna Caroline E. Dahl; Philippe Derreumaux, Mark S.P Sansom and Marc Baaden
Unitymol is a molecular editor, viewer and prototyping platform, coded in C# with the Unity3D game engine. It's initial version was developed by Zhihan Lv, Alex Tek, Franck da Silva, Charly Empereur-mot, Matthieu Chavent and Marc Baaden. Unitymol includes Hyperballs designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg).
GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks and hyperboloids by Matthieu Chavent, Antoine Vanel, Alex Tek, Bruno Levy, Sophie Robert, Bruno Raffin and Marc Baaden