Tools
Quantum Espresso
http://www.quantum-espresso.org/
TurboRVB
http://people.sissa.it/~sorella/web/
Software for analysing transmission electron microscope images and density maps of macromolecular complexes based on normal mode analysis. Author S. Jonic (For details please see http://www-ext.impmc.upmc.fr/~jonic/)
SEGHCA
Division of a protein sequence into foldable domains.
Authors: G. Faure, I. Callebaut
TREMOLOHCA
analysis of the domain architecture and hydrophobic conservation in similarity searches.
Authors: G. Faure, I. Callebaut
TEF 2.0
division of a protein structure into optimal closed loops
http://www.stratmann.fr/software/tef/
Web-server: http://bioserv.rpbs.univ-paris-diderot.fr/
Authors : D. Stratmann, J.S. Pathmanathan, J. Chomilier
CS-HADDOCK
Quantitative use of chemical shifts for the modeling of protein complexes
https://www.wenmr.eu/wenmr/CS-HADDOCK
Authors : D. Stratmann, R. Boelens, A.M.J.J. Bonvin
NOEnet
Use of NOE networks for NMR resonance assignment of proteins with known 3D structure
http://www.icsn.cnrs-gif.fr/download/nmr
Authors : D. Stratmann, E. Guittet, C. v. Heijenoort
RPBS
Softwares available on the RPBS server (Web interface)
http://bioserv.rpbs.univ-paris-diderot.fr/
MIR
Most Interacting Residues, Monte Carlo prediction of core hydrophobic amino acids.
Web server: http://mobyle.rpbs.univ-paris-diderot.fr
Authors : J. Chomilier
SPROUTS
Free energy variations upon mutations
Web server: http://sprouts.rpbs.univ-paris-diderot.fr
Authors : J. Chomilier, M. Lonquety
PIVclustering
Structural cluster analysis of atomic structures (from databases or simulations, e.g., MD trajectories). Target systems include crystals, amorphous materials, liquids, solutions, and isolated clusters. The distance metric is based on Permutation Invariant Vectors (PIV) (J.Chem.Phys. 139, 074101 (2013)) or SPRINT topological coordinates (Phys.Rev.Lett. 107, 085504 (2011)). Documentation and download: http://sourceforge.net/projects/pivclustering
Authors: G.A. Gallet, F. Pietrucci