Members
Overall Objectives
Research Program
Highlights of the Year
New Software and Platforms
New Results
Partnerships and Cooperations
Dissemination
Bibliography
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Bibliography

Major publications by the team in recent years
[1]
F. Cazals, P. Kornprobst (editors)
Modeling in Computational Biology and Medicine: A Multidisciplinary Endeavor, Springer, 2013. [ DOI : 10.1007/978-3-642-31208-3 ]
http://hal.inria.fr/hal-00845616
[2]
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.
http://hal.inria.fr/hal-00849873
[3]
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.
[4]
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.
[5]
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.
[6]
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.
[7]
F. Cazals, C. Karande.
An algorithm for reporting maximal c-cliques, in: Theoretical Computer Science, 2005, vol. 349, no 3, pp. 484–490.
[8]
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.
[9]
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.
[10]
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.
[11]
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

[12]
D. Agarwal.
Topics in mass spectrometry based structure determination, Université Nice Sophia Antipolis, May 2015.
https://tel.archives-ouvertes.fr/tel-01176554
[13]
A. Lhéritier.
Nonparametric Methods for Learning and Detecting Multivariate Statistical Dissimilarity, Université Nice Sophia Antipolis, November 2015.
https://hal.inria.fr/tel-01245946

Articles in International Peer-Reviewed Journals

[14]
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 ]
https://hal.inria.fr/hal-01245401
[15]
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 ]
https://hal.inria.fr/hal-01259806
[16]
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.
https://hal.archives-ouvertes.fr/hal-01245395

International Conferences with Proceedings

[17]
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.
https://hal.inria.fr/hal-01245408

Internal Reports

[18]
F. Cazals, A. Lhéritier.
Beyond Two-sample-tests: Localizing Data Discrepancies in High-dimensional Spaces, Inria, March 2015, no RR-8734, 29 p.
https://hal.inria.fr/hal-01159235
[19]
A. Lhéritier, F. Cazals.
A Sequential Nonparametric Two-Sample Test, Inria, March 2015, no RR-8704, 18 p.
https://hal.inria.fr/hal-01135608
[20]
S. Marillet, P. Boudinot, F. Cazals.
High Resolution Crystal Structures Leverage Protein Binding Affinity Predictions, Inria, March 2015, no RR-8733.
https://hal.inria.fr/hal-01159641
[21]
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.
https://hal.inria.fr/hal-01191462
[22]
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.
https://hal.inria.fr/hal-01191028
References in notes
[23]
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.
[24]
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.
[25]
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.
[26]
O. Becker, A. D. Mackerell, B. Roux, M. Watanabe.
Computational Biochemistry and Biophysics, M. Dekker, 2001.
[27]
A.-C. Camproux, R. Gautier, P. Tuffery.
A Hidden Markov Model derived structural alphabet for proteins, in: J. Mol. Biol., 2004, pp. 591-605.
[28]
M. L. Connolly.
Analytical molecular surface calculation, in: J. Appl. Crystallogr., 1983, vol. 16, no 5, pp. 548–558.
[29]
R. Dunbrack.
Rotamer libraries in the 21st century, in: Curr Opin Struct Biol, 2002, vol. 12, no 4, pp. 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, pp. 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), M. G. Rossmann, E. Arnold (editors), Springer, 2001, pp. 531–539.
[33]
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.
[34]
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.
[35]
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.
[36]
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.
[37]
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.
[38]
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.
[39]
M. Pettini.
Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics, Springer, 2007.
[40]
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.
[41]
D. Rajamani, S. Thiel, S. Vajda, C. Camacho.
Anchor residues in protein-protein interactions, in: PNAS, 2004, vol. 101, no 31, pp. 11287-11292.
[42]
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.
[43]
F. Richards.
Areas, volumes, packing and protein structure, in: Ann. Rev. Biophys. Bioeng., 1977, vol. 6, pp. 151-176.
[44]
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.
[45]
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.
[46]
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.
[47]
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.
[48]
S. Wodak, J. Janin.
Structural basis of macromolecular recognition, in: Adv. in protein chemistry, 2002, vol. 61, pp. 9–73.