Section: Software

Software

This section briefly comments on all the software distributed by ABS . On the one hand, the software released in 2012 is briefly described as the context is presented in the sections dedicated to new results. On the other hand, the software made available before 2012 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 for Mass Spectrometry Data

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

Context. Our work on the stoichiometry determination (SD) problem for noisy data in structural proteomics is described in section 6.2.1 . 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/voratom/ .

vorpatch and compatch : Modeling and Comparing Protein Binding Patches

Participants : Frédéric Cazals, Noël Malod-Dognin.

Context. Modeling protein binding patches 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 protein complex, vorpatch compute the binding patches, while the program compatch allows comparing two patches.

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 thee reconstruction results, we introduced TOleranced Model (TOM) framework, which inherently accommodates uncertainties on the shape and position of proteins. 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/ .

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

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 : theEasy 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.

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