Bibliography

Major publications by the team in recent years

• 1B. 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, n^o 3, pp. 677–692.
• 2F. Cazals.
  Effective nearest neighbors searching on the hyper-cube, with applications to molecular clustering, in: Proc. 14th Annu. ACM Sympos. Comput. Geom., 1998, pp. 222–230.
• 3F. 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.
• 4F. Cazals, T. Dreyfus.
  Multi-scale Geometric Modeling of Ambiguous Shapes with Toleranced Balls and Compoundly Weighted $\alpha$-shapes, in: Symposium on Geometry Processing, Lyon, B. Levy, O. Sorkine (editors), 2010, pp. 1713-1722, Also as Inria Tech report 7306.
• 5F. 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.
• 6F. Cazals, C. Karande.
  An algorithm for reporting maximal $c$-cliques, in: Theoretical Computer Science, 2005, vol. 349, n^o 3, pp. 484–490.
• 7F. 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, n^o 6-7, pp. 551–565, Preliminary version as Inria Tech report 6049.
• 8F. Cazals, F. Proust, R. Bahadur, J. Janin.
  Revisiting the Voronoi description of Protein-Protein interfaces, in: Protein Science, 2006, vol. 15, n^o 9, pp. 2082–2092.
• 9T. Dreyfus, V. Doye, F. Cazals.
  Assessing the Reconstruction of Macro-molecular Assemblies with Toleranced Models, in: Proteins: structure, function, and bioinformatics, 2012, vol. 80, n^o 9, pp. 2125–2136.
• 10S. 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, n^o 2, pp. 487–498.
• 11N. Malod-Dognin, A. Bansal, F. Cazals.
  Characterizing the Morphology of Protein Binding Patches, in: Proteins: structure, function, and bioinformatics, 2012, vol. 80, n^o 12, pp. 2652–2665.

Publications of the year

Articles in International Peer-Reviewed Journals

• 12S. Bornelöv, S. Marillet, J. Komorowski.
  Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers, in: BMC Bioinformatics, 2014, vol. 15, n^o 1, 139 p.
  https://hal.inria.fr/hal-00995110
• 13F. Cazals, T. Dreyfus, S. Sachdeva, N. Shah.
  Greedy Geometric Algorithms for Collection of Balls, with Applications to Geometric Approximation and Molecular Coarse-Graining, in: Computer Graphics Forum, 2014, vol. 33, pp. 1 - 17. [ DOI : 10.1111/cgf.12270 ]
  https://hal.inria.fr/hal-01110229

Internal Reports

• 14D. Agarwal, C. Caillouet, D. Coudert, F. Cazals.
  Unveiling Contacts within Macro-molecular assemblies by solving Minimum Weight Connectivity Inference Problems, Inria, October 2014, n^o RR-8622.
  https://hal.archives-ouvertes.fr/hal-01078378
• 15F. Cazals, T. Dreyfus, D. Mazauric, A. Roth, C. Robert.
  Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison, Inria, October 2014, n^o RR-8610.
  https://hal.archives-ouvertes.fr/hal-01076317
• 16F. Cazals, D. Mazauric.
  Mass Transportation Problems with Connectivity Constraints, with Applications to Energy Landscape Comparison, Inria Sophia Antipolis, October 2014, n^o RR-8611.
  https://hal.archives-ouvertes.fr/hal-01090705

References in notes

• 17F. 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.
• 18F. 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, n^o 7170, pp. 695–701.
• 19F. 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.
• 20O. Becker, A. D. Mackerell, B. Roux, M. Watanabe.
  Computational Biochemistry and Biophysics, M. Dekker, 2001.
• 21A.-C. Camproux, R. Gautier, P. Tuffery.
  A Hidden Markov Model derived structural alphabet for proteins, in: J. Mol. Biol., 2004, pp. 591-605.
• 22M. L. Connolly.
  Analytical molecular surface calculation, in: J. Appl. Crystallogr., 1983, vol. 16, n^o 5, pp. 548–558.
• 23R. Dunbrack.
  Rotamer libraries in the 21st century, in: Curr Opin Struct Biol, 2002, vol. 12, n^o 4, pp. 431-440.
• 24A. 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.
• 25A. Fersht.
  Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Freeman, 1999.
• 26M. 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.
• 27H. Gohlke, G. Klebe.
  Statistical potentials and scoring functions applied to protein-ligand binding, in: Curr. Op. Struct. Biol., 2001, vol. 11, pp. 231-235.
• 28J. 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.
• 29V. K. Krivov, M. Karplus.
  Hidden complexity of free energy surfaces for peptide (protein) folding, in: PNAS, 2004, vol. 101, n^o 41, pp. 14766-14770.
• 30E. 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.
• 31I. Mihalek, O. Lichtarge.
  On Itinerant Water Molecules and Detectability of Protein-Protein Interfaces through Comparative Analysis of Homologues, in: JMB, 2007, vol. 369, n^o 2, pp. 584–595.
• 32J. 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.
• 33M. Pettini.
  Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics, Springer, 2007.
• 34E. 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, n^o 4, pp. 897–907.
• 35D. Rajamani, S. Thiel, S. Vajda, C. Camacho.
  Anchor residues in protein-protein interactions, in: PNAS, 2004, vol. 101, n^o 31, pp. 11287-11292.
• 36D. 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, n^o 1, pp. 57-62.
• 37F. Richards.
  Areas, volumes, packing and protein structure, in: Ann. Rev. Biophys. Bioeng., 1977, vol. 6, pp. 151-176.
• 38G. Rylance, R. Johnston, Y. Matsunaga, C.-B. Li, A. Baba, T. Komatsuzaki.
  Topographical complexity of multidimensional energy landscapes, in: PNAS, 2006, vol. 103, n^o 49, pp. 18551-18555.
• 39G. Schreiber, L. Serrano.
  Folding and binding: an extended family business, in: Current Opinion in Structural Biology, 2005, vol. 15, n^o 1, pp. 1–3.
• 40M. 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.
• 41C. Summa, M. Levitt, W. DeGrado.
  An atomic environment potential for use in protein structure prediction, in: JMB, 2005, vol. 352, n^o 4, pp. 986–1001.
• 42S. Wodak, J. Janin.
  Structural basis of macromolecular recognition, in: Adv. in protein chemistry, 2002, vol. 61, pp. 9–73.