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Section: Software

Software

This section briefly comments on all the software distributed by ABS . On the one hand, the software released in 2011 is briefly described as the context is presented in the sections dedicated to new results. On the other hand, the software made available before 2011 is briefly specified in terms of applications targeted.

In any case, the web page advertising a given software also makes related publications available.

vorpatch and compatch : Modeling and Comparing Protein Binding Patches

Participants : Frédéric Cazals, Noël Malod-Dognin.

Context. Our work on the problem of modeling and comparing atomic resolution protein interfaces has been discussed in sections 6.4.1 and 6.1.1 The programs undertaking these two tasks are respectively named vorpatch and compatch .

Distribution. Binaries for vorpatch and compatch are available from http://cgal.inria.fr/abs/vorpatch-compatch/ .

voratom : Modeling with Toleranced Models

Participants : Frédéric Cazals, Tom Dreyfus.

Context. Our TOleranced Model framework has been described in sections 6.2.1 and 6.2.2 . The corresponding software package includes programs to (i) perform the segmentation of (probability) density maps, (ii) construct toleranced models, (iii) explore toleranced models (geometrically and topologically), (iv) compute Maximal Common Induced Sub-graphs (MCIS) and Maximal Common Edge Sub-graphs (MCES) to assess the pairwise contacts encoded in a TOM.

Distribution. Binaries for the aforementioned programs are made available from http://cgal.inria.fr/abs/voratom/ .

wsheller : Selecting Water Layers in Solvated Protein Structures

Participants : Frédéric Cazals, Christine Roth.

Context. Given a snapshot of a molecular dynamics simulation, a classical problem consists of quenching that structure—minimizing the potential energy of the solute together with selected layers of solvent molecules. The program wsheller provides a solution to the water layer selection, and incorporates a topological control of the layers selected.

Distribution. Binaries for wsheller are available from http://cgal.inria.fr/abs/wsheller/ .

intervor : Modeling Macro-molecular Interfaces

Participant : Frédéric Cazals.

In collaboration with S. Loriot, from the Geometry Factory .

Context. 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. Our 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.

Distribution. The following web site http://cgal.inria.fr/abs/Intervor serves two purposes: on the one hand, calculations can be run from the web site; on the other hand, binaries are distributed for Linux. To the best of our knowledge, this software is the only publicly available one for analyzing Voronoi interfaces in macro-molecular complexes.

vorlume : Computing Molecular Surfaces and Volumes with Certificates

Participant : Frédéric Cazals.

In collaboration with S. Loriot, from the Geometry Factory .

Context. Molecular surfaces and volumes are paramount to molecular modeling, with applications to electrostatic and energy calculations, interface modeling, scoring and model evaluation, pocket and cavity detection, etc. However, for molecular models represented by collections of balls (Van der Waals and solvent accessible models), such calculations are challenging in particular regarding numerics. Because all available programs are overlooking numerical issues, which in particular prevents them from qualifying the accuracy of the results returned, we developed the first certified algorithm, called vorlume . This program is based on so-called certified predicates to guarantee the branching operations of the program, as well as interval arithmetic to return an interval certified to contain the exact value of each statistic of interest—in particular the exact surface area and the exact volume of the molecular model processed.

Distribution. Binaries for Vorlume is available from http://cgal.inria.fr/abs/Vorlume .

ESBTL : theEasy Structural Biology Template Library

Participant : Frédéric Cazals.

In collaboration with S. Loriot (the Geometry Factory), and J. Bernauer, from the EPI AMIB.

Context. The ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric constructions and analyses.

Distribution. The source C++ code is available from http://esbtl.sourceforge.net/ .

A_purva : Comparing Protein Structure by Contact Map Overlap Maximization

Participant : Noël Malod-Dognin.

In collaboration with N. Yanev, University of Sofia, and IMI at Bulgarian Academy of Sciences, Bulgaria, and R. Andonov, INRIA Rennes - Bretagne Atlantique, and IRISA/University of Rennes 1, France.

Context. Structural similarity between proteins provides significant insights about their functions. Maximum Contact Map Overlap maximization (CMO) received sustained attention during the past decade and can be considered today as a credible protein structure measure. The solver A_purva is an exact CMO solver that is both efficient (notably faster than the previous exact algorithms), and reliable (providing accurate upper and lower bounds of the solution). These properties make it applicable for large-scale protein comparison and classification.

Distribution. The software is available from http://apurva.genouest.org .