- gEMfitter – a template-based highly parallel GPU-accelerated program for multiresolution fitting of macromolecular structures developed at INRIA Nancy. It runs in multi-thread and multi-process mode to use all avaliable CPU cores and GPUs in a single workstation or a multi-node cluster for the demanding 3D correlation computation.
- gEMpicker – a template-based highly parallel GPU-accelerated particle picking program developed at INRIA Nancy. It runs in multi-thread and multi-process mode to use all avaliable CPU cores and GPUs in a single workstation or a multi-node cluster for the demanding 2D correlation computation.
- SAM – New “symmetry assembler” program. Available soon.
- HermiteFit – a new docking algorithm for rapid fitting atomic structures into low-to-mid resolution (e.g. cryo-EM) density maps using 3D orthogonal Hermite functions. Available soon.
- DockTrina – a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers.
- RigidRMSD – a library for rapid computations of the root mean square deviations (RMSDs) corresponding to a set of rigid body transformations of a coordinate vector (which can be a molecule in PDB format, for example).
- SAMSON – a software platform for modeling and simulation of nanosystems (SAMSON stands for “Software for Adaptive Modeling and Simulation Of Nanosystems”). SAMSON will integrate algorithms developed in the NANO-D and Orpailleur group. Available soon.
- KBDOCK – a 3D database system that defines and spatially clusters protein binding sites for knowledge-based protein docking. KBDOCK combines the PFAM domain classification with coordinate data from the PDB to analyse the spatial arrangements of domain-domain interactions (DDIs) and domain-peptide interactions (DPIs) by Pfam family, and to propose structural templates for protein docking.
- Kpax – a fast protein structure database search and alignment program. It uses Gaussian functions to score very rapidly the local and spatial environment of each amino acid residue in a protein, and it uses dynamic programming to find the optimal global alignment of two proteins according to their Gaussian similarity scores. This approach allows very fast searches of structural databases, and it allows three-dimensional superpositions of proteins to be calculated rapidly.