## 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.