Team abs
Members
Overall Objectives
Scientific Foundations
Software
New Results
Other Grants and Activities
Dissemination
Bibliography
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Bibliography

Major publications by the team in recent years

[1]
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
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=17237048.
[2]
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
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=18204058.
[3]
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
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=16204845.
[4]
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.
[5]
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.
[6]
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.
[7]
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.
[8]
F. Cazals, C. Karande.
An algorithm for reporting maximal c -cliques, in: Theoretical Computer Science, 2005, vol. 349, no 3, p. 484–490.
[9]
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.
[10]
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

[11]
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.
[12]
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.
[13]
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

[14]
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
http://hal.inria.fr/inria-00429618/en/.

National Peer-Reviewed Conference/Proceedings

[15]
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
http://hal.inria.fr/inria-00429607/en/.

Workshops without Proceedings

[16]
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)

[17]
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

[18]
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
http://hal.archives-ouvertes.fr/inria-00405478/en/, Technical report.
[19]
F. Cazals, D. Cohen-Steiner.
Reconstructing 3D compact sets, INRIA, 2009, no RR-6868
http://hal.inria.fr/inria-00370208/en/, Research Report.
[20]
F. Cazals, H. Kanhere, S. Loriot.
Computing the Volume of Union of Balls: a Certified Algorithm, INRIA, 2009, no 7013, Technical report.
[21]
F. Cazals, S. Loriot.
Modeling Macro-Molecular Interfaces with Intervor, INRIA, 2009, no 7069, Technical report.

References in notes

[22]
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.
[23]
O. Becker, A. D. Mackerell, B. Roux, M. Watanabe.
Computational Biochemistry and Biophysics, M. Dekker, 2001.
[24]
A.-C. Camproux, R. Gautier, P. Tuffery.
A Hidden Markov Model derived structural alphabet for proteins, in: J. Mol. Biol., 2004, p. 591-605.
[25]
F. Chazal, D. Cohen-Steiner, A. Lieutier.
A Sampling Theory for Compacts in Euclidean Spaces, in: ACM Symp. Comp. Geometry, 2006.
[26]
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.
[27]
D. Cohen-Steiner, H. Edelsbrunner, J. Harer.
Stability of Persistence Diagrams, in: ACM Symp. Comp. Geometry, 2005.
[28]
M. L. Connolly.
Analytical molecular surface calculation, in: J. Appl. Crystallogr., 1983, vol. 16.
[29]
R. Dunbrack.
Rotamer libraries in the 21st century, in: Curr Opin Struct Biol, 2002, vol. 12, no 4, p. 431-440.
[30]
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.
[31]
A. Fersht.
Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Freeman, 1999.
[32]
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).
[33]
J. Giesen, M. John.
The Flow Complex: A Data Structure for Geometric Modeling, in: ACM SODA, 2003.
[34]
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.
[35]
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
http://dx.doi.org/10.1073/pnas.0505425102.
[36]
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.
[37]
V. K. Krivov, M. Karplus.
Hidden complexity of free energy surfaces for peptide (protein) folding, in: PNAS, 2004, vol. 12.
[38]
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.
[39]
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.
[40]
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.
[41]
M. Pettini.
Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics, Springer, 2007.
[42]
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.
[43]
D. Rajamani, S. Thiel, S. Vajda, C. Camacho.
Anchor residues in protein-protein interactions, in: PNAS, 2004, vol. 101, p. 11287-11292.
[44]
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
http://www.pnas.org/cgi/content/abstract/102/1/57.
[45]
F. Richards.
Areas, volumes, packing and protein structure, in: Ann. Rev. Biophys. Bioeng., 1977, vol. 6, p. 151-176.
[46]
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.
[47]
G. Schreiber, L. Serrano.
Folding and binding: an extended family business, in: Current Opinion in Structural Biology, 2005, vol. 15, no 1.
[48]
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.
[49]
C. Summa, M. Levitt, W. DeGrado.
An atomic environment potential for use in protein structure prediction, in: JMB, 2005, vol. 352.
[50]
S. Wodak, J. Janin.
Structural basis of macromolecular recognition, in: Adv. in protein chemistry, 2003, vol. 61.

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