## 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 .