Section: New Results

Software

Investigating Interfaces of Macro-Molecular Complexes with Intervor

Participants : Frédéric Cazals, Sébastien Loriot.

Intervor is a software computing a parameter free representation of macro-molecular interfaces, based on the -complex of the atoms [21] . Given two interacting partners, possibly with water molecules squeezed in-between, Intervor computes an interface model which has the following characteristics: (i) it identifies the atoms of the partners which are in direct contact and those whose interaction is water mediated, (ii) it defines a geometric complex separating the partners, the Voronoi interface, whose geometric and topological descriptions are straightforward (surface area, number of patches, curvature), (iii) it enables the definition of the depth of atoms at the interface, thus going beyond the traditional dissection of an interface into a core and a rim.

These features can be used to investigate correlations between structural parameters and key properties such as the conservation of residues, their polarity, the water dynamics at the interface, mutagenesis data, etc.

Intervor can be run from the web site http://cgal.inria.fr/abs/Intervor , or in stand-alone mode upon downloading the binary file. Plugins are also made available for Visual Molecular Dynamics (VMD) and Pymol.

ESBTL: Easy Structural Biology Template Library

Participants : Julie Bernauer, Frédéric Cazals, Sébastien Loriot.

The ever increasing number of structural biological data calls for robust and efficient software for analysis. ESBTL (Easy Structural Biology Template Library) is a lightweight C++ library that handles PDB data and provides a data structure suitable for geometric analysis and advanced constructions. The parser and data model provided by this ready-to-use header-only library provide adequate treatment of usually discarded information (insertion codes, atom occupancy...) while still being able to detect badly formatted files. The template-based structure enables rapid design of new computational structural biology applications and is fully compatible with the new remediated PDB archive format. It also makes the code easy-to-use while being versatile enough to allow advanced user developments.

ESBTL is freely available under the GNU General Public License from http://esbtl.sf.net . The website provides the source code, examples, code snippets and documentation.