Section: Software

Web services

Modeling macro-molecular interfaces

Participant : Frédéric Cazals.

Modeling the interfaces of macro-molecular complexes is key to improve our understanding of the stability and specificity of such interactions. We proposed a simple parameter-free model for macro-molecular interfaces, which enables a multi-scale investigation —from the atomic scale to the whole interface scale. As discussed in [10] and [11] , this interface model improves the state-of-the-art to (i) identify interface atoms, (ii) define interface patches, (iii) assess the interface curvature, (iv) investigate correlations between the interface geometry and water dynamics / conservation patterns / polarity of residues.

The corresponding software, Intervor , has been made available to the community from the web site http://cgal.inria.fr/abs/Intervor . This software is presented in the following application note [21] . To the best of our knowledge, this code is the only publicly available one for analyzing (Voronoi) interfaces in macro-molecular complexes.

Discrimination between crystallographic and biological protein-protein interactions

Participant : Julie Bernauer.

Knowing the oligomeric state of a protein is necessary to understand its function. This tool, accessible as a webserver http://cgal.inria.fr/DiMoVo , provides a reliable discrimination function to obtain the most favorable state of proteins. See [2] .

Protein-protein docking conformation evaluation

Participant : Julie Bernauer.

Scoring is a crucial part of a protein-protein procedure and having a quantitative function to evaluate conformations is mandatory. This server http://cgal.inria.fr/VorScore provides access to a geometric knowledge-based evaluation function. See [1] for further details.