Papers by Sébastien Loriot
Lecture Notes in Computer Science, 2010
We propose two ways to compute the Delaunay triangulation of points on a sphere, or of rounded po... more We propose two ways to compute the Delaunay triangulation of points on a sphere, or of rounded points close to a sphere, both based on the classic incremental algorithm initially designed for the plane. We use the so-called space of circles as mathematical background for this work. We present a fully robust implementation built upon existing generic algorithms provided by the cgal library. The eciency of the implementation is established by benchmarks.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2000
As of today, a number of flexible docking experiments fail due to the lack of candidate conformat... more As of today, a number of flexible docking experiments fail due to the lack of candidate conformations close from the bound ones. To tackle these difficult cases, which usually feature large re-arrangements, the route of choice consists of pre-generating discrete ensembles of conformers. But for a flexible fragment (rotamer, loop, domain), the fact that the generation of such ensembles does not take into account the whole environment of the fragment (in the whole protein or complex), prevents, in general, to directly relate the conformer energy to the thermodynamic equilibrium between the conformations. This observation calls for the development of methods providing a rather uniform sampling of the conformational space of the fragment, so as retain conformers avoiding obvious steric clashes. But such algorithms face one central difficulty: that of characterizing the conformational space coverage, so as to maximize the diversity of the conformers. This paper makes three contributions in this perspective.
Computational Geometry, 2009
... For example, under mild sampling assumptions, mimicking the medial axis transform of a sample... more ... For example, under mild sampling assumptions, mimicking the medial axis transform of a sampled surface allows one to reconstruct the domain enclosed within this ... The ball/sphere/circle processed is denoted B/S/C. See text for the definition of functions CLP and CSP, and Fig. ...
Computational Geometry, 2009
This paper presents a cgal kernel for algorithms manipulating 3D spheres, circles, and circular a... more This paper presents a cgal kernel for algorithms manipulating 3D spheres, circles, and circular arcs. The paper makes three contributions. First, the design of the kernel concept is developed, following the best practices for the design of kernels geared towards curved objects. Second, we show how two dierent frameworks can be combined: one for the general setting, and one dedicated to the case where all the objects handled are located on a reference sphere. In both cases, the mathematical derivations for predicates and constructions are detailed. Third, an application to the construction of the exact arrangement of circles on a sphere is overviewed.
Bioinformatics, 2010
Intervor is a software computing a parameter-free representation of macro-molecular interfaces, b... more 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. Intervor can be run from the web site http://cgal.inria.fr/abs/Intervor or upon downloading the binary file. Plugins are also made available for VMD and Pymol.
Bioinformatics, 2010
The ever increasing number of structural biological data calls for robust and efficient software ... more 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.) while still being able to detect badly formatted files. The template-based structure allows rapid design of new computational structural biology applications and is fully compatible with the new remediated PDB archive format. It also allows the code to be 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 web site provides the source code, examples, code snippets and documentation.
ACM Transactions on Mathematical Software, 2011
Balls and spheres are amongst the simplest 3D modeling primitives, and computing the volume of a ... more Balls and spheres are amongst the simplest 3D modeling primitives, and computing the volume of a union of balls is an elementary problem. Although a number of strategies addressing this problem have been investigated in several communities, we are not aware of any robust algorithm, and present the first such algorithm. Our calculation relies on the decomposition of the volume
We propose two approaches for computing the Delaunay triangulation of points on a sphere, or of r... more We propose two approaches for computing the Delaunay triangulation of points on a sphere, or of rounded points close to a sphere, both based on the classic incremental algorithm initially designed for the plane. The space of circles gives the mathematical background for this work. We implemented the two approaches in a fully robust way, building upon existing generic algorithms provided by the cgal library. The effciency and scalability of the method is shown by benchmarks.
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Papers by Sébastien Loriot