Team abs

Overall Objectives
Scientific Foundations
New Results
Other Grants and Activities


Major publications by the team in recent years

J. Bernauer, J. Azé, J. Janin, A. Poupon.
A new protein-protein docking scoring function based on interface residue properties., in: Bioinformatics, 2007, vol. 23, no 5, p. 555-62
J. Bernauer, R. Bahadur, F. Rodier, J. Janin, A. Poupon.
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions., in: Bioinformatics, 2008, vol. 24, no 5, p. 652-8
J. Bernauer, A. Poupon, J. Azé, J. Janin.
A docking analysis of the statistical physics of protein-protein recognition., in: Phys Biol, 2005, vol. 2, no 2, p. S17-23
J.-D. Boissonnat, F. Cazals.
Smooth Surface Reconstruction via Natural Neighbour Interpolation of Distance Functions, in: Comp. Geometry Theory and Applications, 2002, p. 185–203.
F. Cazals.
Effective nearest neighbors searching on the hyper-cube, with a pplications to molecular clustering, in: Proc. 14th Annu. ACM Sympos. Comput. Geom., 1998, p. 222–230.
F. Cazals, F. Chazal, T. Lewiner.
Molecular shape analysis based upon the Morse-Smale complex and the Connolly function, in: ACM Symposium on Computational Geometry, San Diego, USA, 2003.
F. Cazals, J. Giesen.
Delaunay Triangulation Based Surface Reconstruction, in: Effective Computational Geometry for curves and surfaces, J.-D. Boissonnat, M. Teillaud (editors), Springer-Verlag, Mathematics and Visualization, 2006.
F. Cazals, C. Karande.
An algorithm for reporting maximal c -cliques, in: Theoretical Computer Science, 2005, vol. 349, no 3, p. 484–490.
F. Cazals, M. Pouget.
Estimating Differential Quantities using Polynomial fitting of Osculating Jets, in: Computer Aided Geometric Design, 2005, vol. 22, no 2, p. 121–146, Conf. version: Symp. on Geometry Processing 2003.
F. Cazals, F. Proust, R. Bahadur, J. Janin.
Revisiting the Voronoi description of Protein-Protein interfaces, in: Protein Science, 2006, vol. 15, no 9, p. 2082–2092.

Publications of the year

Articles in International Peer-Reviewed Journal

B. Bouvier, R. Grunberg, M. Nilges, F. Cazals.
Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics and composition, in: Proteins: structure, function, and bioinformatics, 2009, vol. 76, no 3, p. 677–692.
P. M. M. D. Castro, F. Cazals, S. Loriot, M. Teillaud.
Design of the CGAL Spherical Kernel and application to arrangements of circles on a sphere, in: Computational Geometry: Theory and Applications, 2009, vol. 42, no 6-7, p. 536–550.
F. Cazals, S. Loriot.
Computing the exact arrangement of circles on a sphere, with applications in structural biology, in: Computational Geometry: Theory and Applications, 2009, vol. 42, no 6-7, p. 551–565.

International Peer-Reviewed Conference/Proceedings

T. Bourquard, J. Bernauer, J. Azé, A. Poupon.
Comparing Voronoi and Laguerre tessellations in the protein-protein docking context, in: Sixth annual International Symposium on Voronoi Diagrams, Danemark Copenhagen, F. Anton and J. Andreas Baerentzen - Technical University of Denmark, Danemark Copenhagen, 2009-06-23

National Peer-Reviewed Conference/Proceedings

S. Loriot, F. Cazals, M. Levitt, J. Bernauer.
A geometric knowledge-based coarse-grained scoring potential for structure prediction evaluation, in: Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), France Nantes, Société Française de Bioinformatique, France Nantes, 2009-07

Workshops without Proceedings

F. Cazals, T. Dreyfus.
Assessing the Stability of Protein Complexes within Large Assemblies, in: ISMB Satellite Meeting on Structural Bioinformatics and Computational Biophysics, 2009.

Scientific Books (or Scientific Book chapters)

F. Cazals, F. Chazal, J. Giesen.
Spectral Techniques to Explore Point Clouds in Euclidean Space, with Applications to the Inference of Collective Coordinates in Structural Biology, in: Nonlinear Computational Geometry, I. Emiris, F. Sottile, T. Theobald (editors), The Institute of Mathematics and its Applications, 2009.

Internal Reports

M. Caroli, P. De Castro, S. Loriot, M. Teillaud, C. Wormser.
Robust and Efficient Delaunay triangulations of points on or close to a sphere, INRIA, 2009, no 7004, Technical report.
F. Cazals, D. Cohen-Steiner.
Reconstructing 3D compact sets, INRIA, 2009, no RR-6868, Research Report.
F. Cazals, H. Kanhere, S. Loriot.
Computing the Volume of Union of Balls: a Certified Algorithm, INRIA, 2009, no 7013, Technical report.
F. Cazals, S. Loriot.
Modeling Macro-Molecular Interfaces with Intervor, INRIA, 2009, no 7069, Technical report.

References in notes

R. Bahadur, P. Chakrabarti, F. Rodier, J. Janin.
A dissection of specific and non-specific protein-protein interfaces, in: J. Mol. Biol., 2004, vol. 336.
O. Becker, A. D. Mackerell, B. Roux, M. Watanabe.
Computational Biochemistry and Biophysics, M. Dekker, 2001.
A.-C. Camproux, R. Gautier, P. Tuffery.
A Hidden Markov Model derived structural alphabet for proteins, in: J. Mol. Biol., 2004, p. 591-605.
F. Chazal, D. Cohen-Steiner, A. Lieutier.
A Sampling Theory for Compacts in Euclidean Spaces, in: ACM Symp. Comp. Geometry, 2006.
F. Chazal, A. Lieutier.
Weak Feature Size and persistent homology : computing homology of solids in Im3 $\#8477 ^n$ from noisy data samples, in: ACM SoCG, 2005, p. 255-262.
D. Cohen-Steiner, H. Edelsbrunner, J. Harer.
Stability of Persistence Diagrams, in: ACM Symp. Comp. Geometry, 2005.
M. L. Connolly.
Analytical molecular surface calculation, in: J. Appl. Crystallogr., 1983, vol. 16.
R. Dunbrack.
Rotamer libraries in the 21st century, in: Curr Opin Struct Biol, 2002, vol. 12, no 4, p. 431-440.
A. Fernandez, R. Berry.
Extent of Hydrogen-Bond Protection in Folded Proteins: A Constraint on Packing Architectures, in: Biophysical Journal, 2002, vol. 83, p. 2475-2481.
A. Fersht.
Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Freeman, 1999.
M. Gerstein, F. Richards.
Protein geometry: volumes, areas, and distances, in: The international tables for crystallography (Vol F, Chap. 22), 2001, vol. F (Chapter 22.1.1).
J. Giesen, M. John.
The Flow Complex: A Data Structure for Geometric Modeling, in: ACM SODA, 2003.
H. Gohlke, G. Klebe.
Statistical potentials and scoring functions applied to protein-ligand binding, in: Curr. Op. Struct. Biol., 2001, vol. 11, p. 231-235.
M. Guharoy, P. Chakrabarti.
Conservation and relative importance of residues across protein-protein interfaces., in: Proc Natl Acad Sci U S A, Oct 2005, vol. 102, no 43, p. 15447–15452
J. Janin, S. Wodak, M. Levitt, B. Maigret.
Conformations of amino acid side chains in proteins, in: J. Mol. Biol., 1978, vol. 125, p. 357–386.
V. K. Krivov, M. Karplus.
Hidden complexity of free energy surfaces for peptide (protein) folding, in: PNAS, 2004, vol. 12.
E. Meerbach, C. Schutte, I. Horenko, B. Schmidt.
Metastable Conformational Structure and Dynamics: Peptides between Gas Phase and Aqueous Solution, in: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics 87, O. Kuhn, L. Wudste (editors), Springer, 2007.
I. Mihalek, O. Lichtarge.
On Itinerant Water Molecules and Detectability of Protein-Protein Int erfaces through Comparative Analysis of Homologues, in: JMB, 2007, vol. 369, no 2.
J. Mintseris, B. Pierce, K. Wiehe, R. Anderson, R. Chen, Z. Weng.
Integrating statistical pair potentials into protein complex prediction, in: Proteins, 2007, vol. 69, p. 511–520.
M. Pettini.
Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics, Springer, 2007.
E. Plaku, H. Stamati, C. Clementi, L. Kavraki.
Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction, in: Proteins: Structure, Function, and Bioinformatics, 2007, vol. 67, no 4, p. 897–907.
D. Rajamani, S. Thiel, S. Vajda, C. Camacho.
Anchor residues in protein-protein interactions, in: PNAS, 2004, vol. 101, p. 11287-11292.
D. Reichmann, O. Rahat, S. Albeck, R. Meged, O. Dym, G. Schreiber.
From The Cover: The modular architecture of protein-protein binding interfaces, in: PNAS, 2005, vol. 102, no 1, p. 57-62
F. Richards.
Areas, volumes, packing and protein structure, in: Ann. Rev. Biophys. Bioeng., 1977, vol. 6, p. 151-176.
G. Rylance, R. Johnston, Y. Matsunaga, C.-B. Li, A. Baba, T. Komatsuzaki.
Topographical complexity of multidimensional energy landscapes, in: PNAS, 2006, vol. 103, no 49, p. 18551-18555.
G. Schreiber, L. Serrano.
Folding and binding: an extended family business, in: Current Opinion in Structural Biology, 2005, vol. 15, no 1.
M. Sippl.
Calculation of Conformational Ensembles from Potential of Mean Force: An Approach to the Knowledge-based prediction of Local Structures in Gobular Proteins, in: J. Mol. Biol., 1990, vol. 213, p. 859-883.
C. Summa, M. Levitt, W. DeGrado.
An atomic environment potential for use in protein structure prediction, in: JMB, 2005, vol. 352.
S. Wodak, J. Janin.
Structural basis of macromolecular recognition, in: Adv. in protein chemistry, 2003, vol. 61.