On the characterization and selection of diverse conformational ensembles with applications to flexible docking.

To address challenging flexible docking problems, a number of docking algorithms pregenerate large collections of candidate conformers. To remove the redundancy from such ensembles, a central problem in this context is to report a selection of conformers maximizing some geometric diversity criterion. We make three contributions to this problem.

ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules.

Unlabelled: The ever increasing number of structural biological data calls for robust and efficient software for analysis. Easy Structural Biology Template Library (ESBTL) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric constructions and analyses. The parser and data model provided by this ready-to-use include-only library allows adequate treatment of usually discarded information (insertion code, atom occupancy, etc.

Modeling macro-molecular interfaces with Intervor.

Summary: Intervor is a software computing a parameter-free representation of macro-molecular interfaces, based on the alpha-complex of the atoms. Given two interacting partners, possibly with water molecules squeezed in-between them, 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 allows 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.