Overall Objectives
Research Program
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
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Major publications by the team in recent years
F. Cazals, P. Kornprobst (editors)
Modeling in Computational Biology and Medicine: A Multidisciplinary Endeavor, Springer, 2013. [ DOI : 10.1007/978-3-642-31208-3 ]
D. Agarwal, J. Araujo, C. Caillouet, F. Cazals, D. Coudert, S. Pérennes.
Connectivity Inference in Mass Spectrometry based Structure Determination, in: European Symposium on Algorithms (Springer LNCS 8125), Sophia Antipolis, France, H. Bodlaender, G. Italiano (editors), Springer, 2013, pp. 289–300.
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, pp. 677–692.
F. Cazals, F. Chazal, T. Lewiner.
Molecular shape analysis based upon the Morse-Smale complex and the Connolly function, in: ACM SoCG, San Diego, USA, 2003, pp. 351-360.
F. Cazals, T. Dreyfus.
Multi-scale Geometric Modeling of Ambiguous Shapes with Toleranced Balls and Compoundly Weighted α-shapes, in: Symposium on Geometry Processing, Lyon, B. Levy, O. Sorkine (editors), 2010, pp. 1713-1722, Also as Inria Tech report 7306.
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, pp. 484–490.
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, pp. 551–565, Preliminary version as Inria Tech report 6049.
T. Dreyfus, V. Doye, F. Cazals.
Assessing the Reconstruction of Macro-molecular Assemblies with Toleranced Models, in: Proteins: structure, function, and bioinformatics, 2012, vol. 80, no 9, pp. 2125–2136.
S. Loriot, S. Sachdeva, K. Bastard, C. Prevost, F. Cazals.
On the Characterization and Selection of Diverse Conformational Ensembles, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, vol. 8, no 2, pp. 487–498.
N. Malod-Dognin, A. Bansal, F. Cazals.
Characterizing the Morphology of Protein Binding Patches, in: Proteins: structure, function, and bioinformatics, 2012, vol. 80, no 12, pp. 2652–2665.
Publications of the year

Doctoral Dissertations and Habilitation Theses

D. Agarwal.
Topics in mass spectrometry based structure determination, Université Nice Sophia Antipolis, May 2015.
A. Lhéritier.
Nonparametric Methods for Learning and Detecting Multivariate Statistical Dissimilarity, Université Nice Sophia Antipolis, November 2015.

Articles in International Peer-Reviewed Journals

D. Agarwal, C. Caillouet, D. Coudert, F. Cazals.
Unveiling Contacts within Macro-molecular assemblies by solving Minimum Weight Connectivity Inference Problems, in: Molecular and Cellular Proteomics, April 2015, 27 p. [ DOI : 10.1074/mcp.M114.047779 ]
J.-D. Boissonnat, D. Mazauric.
On the complexity of the representation of simplicial complexes by trees, in: Theoretical Computer Science, February 2016, vol. 617, 17 p. [ DOI : 10.1016/j.tcs.2015.12.034 ]
F. Cazals, T. Dreyfus, D. Mazauric, A. Roth, C. Robert.
Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison, in: Journal of Computational Chemistry, May 2015, vol. 36, no 6, 18 p.

International Conferences with Proceedings

F. Cazals, A. Lhéritier.
Beyond Two-sample-tests: Localizing Data Discrepancies in High-dimensional Spaces, in: IEEE/ACM International Conference on Data Science and Advanced Analytics, Paris, France, P. Gallinari, J. Kwok, G. Pasi, O. Zaiane (editors), October 2015, 29 p.

Internal Reports

F. Cazals, A. Lhéritier.
Beyond Two-sample-tests: Localizing Data Discrepancies in High-dimensional Spaces, Inria, March 2015, no RR-8734, 29 p.
A. Lhéritier, F. Cazals.
A Sequential Nonparametric Two-Sample Test, Inria, March 2015, no RR-8704, 18 p.
S. Marillet, P. Boudinot, F. Cazals.
High Resolution Crystal Structures Leverage Protein Binding Affinity Predictions, Inria, March 2015, no RR-8733.
S. Marillet, M.-P. Lefranc, P. Boudinot, F. Cazals.
Dissecting Interfaces of Antibody -Antigen Complexes: from Ligand Specific Features to Binding Affinity Predictions, Inria Sophia Antipolis, September 2015, no RR-8770, 61 p.
A. Roth, T. Dreyfus, C. H. Robert, F. Cazals.
Hybridizing rapidly growing random trees and basin hopping yields an improved exploration of energy landscapes, Inria, September 2015, no RR-8768, 29 p.
References in notes
F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B. Chait, M. Rout, A. Sali.
Determining the architectures of macromolecular assemblies, in: Nature, Nov 2007, vol. 450, pp. 683-694.
F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B. Chait, A. Sali, M. Rout.
The molecular architecture of the nuclear pore complex, in: Nature, 2007, vol. 450, no 7170, pp. 695–701.
F. Alber, F. Förster, D. Korkin, M. Topf, A. Sali.
Integrating Diverse Data for Structure Determination of Macromolecular Assemblies, in: Ann. Rev. Biochem., 2008, vol. 77, pp. 11.1–11.35.
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, pp. 591-605.
M. L. Connolly.
Analytical molecular surface calculation, in: J. Appl. Crystallogr., 1983, vol. 16, no 5, pp. 548–558.
R. Dunbrack.
Rotamer libraries in the 21st century, in: Curr Opin Struct Biol, 2002, vol. 12, no 4, pp. 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, pp. 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), M. G. Rossmann, E. Arnold (editors), Springer, 2001, pp. 531–539.
H. Gohlke, G. Klebe.
Statistical potentials and scoring functions applied to protein-ligand binding, in: Curr. Op. Struct. Biol., 2001, vol. 11, pp. 231-235.
J. Janin, S. Wodak, M. Levitt, B. Maigret.
Conformations of amino acid side chains in proteins, in: J. Mol. Biol., 1978, vol. 125, pp. 357–386.
V. K. Krivov, M. Karplus.
Hidden complexity of free energy surfaces for peptide (protein) folding, in: PNAS, 2004, vol. 101, no 41, pp. 14766-14770.
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 Interfaces through Comparative Analysis of Homologues, in: JMB, 2007, vol. 369, no 2, pp. 584–595.
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, pp. 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, pp. 897–907.
D. Rajamani, S. Thiel, S. Vajda, C. Camacho.
Anchor residues in protein-protein interactions, in: PNAS, 2004, vol. 101, no 31, pp. 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, pp. 57-62.
F. Richards.
Areas, volumes, packing and protein structure, in: Ann. Rev. Biophys. Bioeng., 1977, vol. 6, pp. 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, pp. 18551-18555.
G. Schreiber, L. Serrano.
Folding and binding: an extended family business, in: Current Opinion in Structural Biology, 2005, vol. 15, no 1, pp. 1–3.
M. Sippl.
Calculation of Conformational Ensembles from Potential of Mean Force: An Approach to the Knowledge-based prediction of Local Structures in Globular Proteins, in: J. Mol. Biol., 1990, vol. 213, pp. 859-883.
C. Summa, M. Levitt, W. DeGrado.
An atomic environment potential for use in protein structure prediction, in: JMB, 2005, vol. 352, no 4, pp. 986–1001.
S. Wodak, J. Janin.
Structural basis of macromolecular recognition, in: Adv. in protein chemistry, 2002, vol. 61, pp. 9–73.