Section: Software and Platforms

Software

This section briefly comments on all the software distributed by ABS . On the one hand, the software released in 2013 is briefly described as the context is presented in the sections dedicated to new results. On the other hand, the software made available before 2013 is briefly specified in terms of applications targeted.

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

addict : Stoichiometry Determination from Mass Spectrometry Data

Participants : Deepesh Agarwal, Frédéric Cazals, Noël Malod-Dognin.

Context. Given the individual masses of the proteins present in a complex, together with the mass of that complex, stoichiometry determination (SD) consists of computing how many copies of each protein are needed to account for the overall mass of the complex. Our work on the stoichiometry determination (SD) problem for noisy data in structural proteomics is described in [17] . The addict software suite not only implements our algorithms DP++ and DIOPHANTINE , but also important algorithms to determine the so-called Frobenius number of a vector of protein masses, and also to estimate the number of solutions of a SD problem, from an unbounded knapsack problem.

Distribution. Binaries for the addict software suite are made available from http://team.inria.fr/abs/software/addict/ .

vorpatch and compatch : Modeling and Comparing Protein Binding Patches

Participants : Frédéric Cazals, Noël Malod-Dognin.

Context. Modeling protein binding patches, i.e. the sets of atoms responsible of an interaction, is a central problem to foster our understanding of the stability and of the specificity of macro-molecular interactions. We developed a binding patch model which encodes morphological properties, allows an atomic-level comparison of binding patches at the geometric and topological levels, and allows estimating binding affinities—with state-of-the-art results on the protein complexes of the binding affinity benchmark. Given a binary protein complex, vorpatch identifies the binding patches, and computes a topological encoding of each patch, defined as an atom shelling tree generalizing the core-rim model. The program compatch allows comparing two patches via the comparison of their atom shelling trees, by favoring either a geometric or a topological comparison.

Distribution. Binaries for VORPATCH and COMPATCH are available from http://team.inria.fr/abs/software/vorpatch-compatch .

voratom : Modeling Protein Assemblies with Toleranced Models

Participants : Frédéric Cazals, Tom Dreyfus.

Context. Large protein assemblies such as the Nuclear Pore Complex (NPC), chaperonin cavities, the proteasome or ATP synthases, to name a few, are key to numerous biological functions. Modeling such assemblies is especially challenging due to their plasticity (the proteins involved may change along the cell cycle), their size, and also the flexibility of the sub-units. To cope with these difficulties, a reconstruction strategy known as Reconstruction by Data Integration (RDI), aims at integrating diverse experimental data. But the uncertainties on the input data yield equally uncertain reconstructed models, calling for quantitative assessment strategies.

To leverage these reconstruction results, we introduced TOleranced Model (TOM) framework, which inherently accommodates uncertainties on the shape and position of proteins represented as density maps — maps from cryo electron-microscopy or maps stemming from reconstruction by data integration. In a TOM, a fuzzy molecule is sandwiched between two union of concentric balls, the size of the region between these two unions conveying information on the uncertainties.

The corresponding software package, VORATOM , 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 software package VORATOM are made available from http://team.inria.fr/abs/software/voratom/ .

intervor : Modeling Macro-molecular Interfaces

Participant : Frédéric Cazals.

In collaboration with S. Loriot (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 website http://team.inria.fr/abs/software/intervor serves two purposes: on the one hand, calculations can be run from the website; on the other hand, binaries are made available. 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 (The Geometry Factory , France)

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://team.inria.fr/abs/software/vorlume .

ESBTL : the Easy Structural Biology Template Library

Participant : Frédéric Cazals.

In collaboration with S. Loriot (The Geometry Factory , France) and J. Bernauer (Inria AMIB, France).

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, such as those proposed by INTERVOR , VORPATCH and COMPATCH .

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