## 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/.