Bibliography

Major publications by the team in recent years

• 1F. 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
• 2D. 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
• 3D. 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, 2015, vol. 14, pp. 2274–2282. [ DOI : 10.1074/mcp.M114.047779 ]
  https://hal.archives-ouvertes.fr/hal-01078378
• 4J. Carr, D. Mazauric, F. Cazals, D. J. Wales.
  Energy landscapes and persistent minima, in: The Journal of Chemical Physics, 2016, vol. 144, n^o 5, 4 p. [ DOI : 10.1063/1.4941052 ]
  https://www.repository.cam.ac.uk/handle/1810/253412
• 5F. 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.
• 6F. Cazals, T. Dreyfus, D. Mazauric, A. Roth, C. Robert.
  Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison, in: J. of Computational Chemistry, 2015, vol. 36, n^o 16, pp. 1213–1231. [ DOI : 10.1002/jcc.23913 ]
  https://hal.archives-ouvertes.fr/hal-01076317
• 7F. Cazals, T. Dreyfus, S. Sachdeva, N. Shah.
  Greedy Geometric Algorithms for Collections of Balls, with Applications to Geometric Approximation and Molecular Coarse-Graining, in: Computer Graphics Forum, 2014, vol. 33, n^o 6, pp. 1–17. [ DOI : 10.1111/cgf.12270 ]
  http://hal.inria.fr/hal-00777892
• 8F. Cazals, C. Karande.
  An algorithm for reporting maximal $c$-cliques, in: Theoretical Computer Science, 2005, vol. 349, n^o 3, pp. 484–490.
• 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.
• 10T. Dreyfus, V. Doye, F. Cazals.
  Probing a Continuum of Macro-molecular Assembly Models with Graph Templates of Sub-complexes, in: Proteins: structure, function, and bioinformatics, 2013, vol. 81, n^o 11, pp. 2034–2044. [ DOI : 10.1002/prot.24313 ]
  http://hal.inria.fr/hal-00849795
• 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.
• 12S. Marillet, P. Boudinot, F. Cazals.
  High Resolution Crystal Structures Leverage Protein Binding Affinity Predictions, in: Proteins: structure, function, and bioinformatics, 2015, vol. 1, n^o 84, pp. 9–20. [ DOI : 10.1002/prot.24946 ]
  https://hal.inria.fr/hal-01159641
• 13A. Roth, T. Dreyfus, C. Robert, F. Cazals.
  Hybridizing rapidly growing random trees and basin hopping yields an improved exploration of energy landscapes, in: J. Comp. Chem., 2016, vol. 37, n^o 8, pp. 739–752. [ DOI : 10.1002/jcc.24256 ]
  https://hal.inria.fr/hal-01191028

Publications of the year

Articles in International Peer-Reviewed Journals

• 14P. Bonami, D. Mazauric, Y. Vaxès.
  Maximum flow under proportional delay constraint, in: Theoretical Computer Science, 2017, vol. 689, pp. 58-66. [ DOI : 10.1016/j.tcs.2017.05.034 ]
  https://hal.inria.fr/hal-01571232
• 15F. Cazals, T. Dreyfus.
  The Structural Bioinformatics Library: modeling in biomolecular science and beyond, in: Bioinformatics, April 2017, vol. 33, n^o 8. [ DOI : 10.1093/bioinformatics/btw752 ]
  https://hal.inria.fr/hal-01570848
• 16S. Fleischer, S. Ries, P. Shen, A. Lhéritier, F. Cazals, G. R. Burmester, T. Dörner, S. Fillatreau.
  Anti-interleukin-6 signalling therapy rebalances the disrupted cytokine production of B cells from patients with active rheumatoid arthritis, in: European Journal of Immunology, September 2017. [ DOI : 10.1002/eji.201747191 ]
  https://hal.inria.fr/hal-01671956
• 17S. Marillet, M.-P. Lefranc, P. Boudinot, F. Cazals.
  Novel Structural Parameters of Ig–Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity, in: Frontiers in Immunology, February 2017, vol. 8. [ DOI : 10.3389/fimmu.2017.00034 ]
  https://hal.inria.fr/hal-01570846

International Conferences with Proceedings

• 18N. Cohen, F. Havet, D. Mazauric, I. Sau, R. Watrigant.
  Complexity Dichotomies for the Minimum F -Overlay Problem, in: IWOCA 2017 - 28th International Workshop on Combinatorial Algorithms, Newcastle, Australia, July 2017, 12 p.
  https://hal.inria.fr/hal-01571229
• 19N. Lascano, G. Gallardo, R. Deriche, D. Mazauric, D. Wassermann.
  Extracting the Groupwise Core Structural Connectivity Network: Bridging Statistical and Graph-Theoretical Approaches, in: Information Processing in Medical Imaging, Boone, United States, 2017, https://arxiv.org/abs/1701.01311.
  https://hal.inria.fr/hal-01426870

Internal Reports

• 20F. Cazals, D. Mazauric, R. Tetley, R. Watrigant.
  Comparing two clusterings using matchings between clusters of clusters, Inria Sophia Antipolis - Méditerranée ; Universite Cote d'Azur, April 2017, n^o RR-9063.
  https://hal.inria.fr/hal-01514872

Scientific Popularization

• 21D. Mazauric.
  Tour de cartes - La magie des graphes et du binaire, 2017, 2 p, Posters expliquant un tour de cartes qui utilise les graphes et le codage binaire.
  https://hal.inria.fr/hal-01671009
• 22D. Mazauric.
  Transmission de pensée - La magie du binaire, 2017, 13 p, Posters expliquant le binaire avec un tour de magie.
  https://hal.inria.fr/hal-01670180

References in notes

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  Determining the architectures of macromolecular assemblies, in: Nature, Nov 2007, vol. 450, pp. 683-694.
• 24F. 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.
• 25F. 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.
• 26O. Becker, A. D. Mackerell, B. Roux, M. Watanabe.
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  A Hidden Markov Model derived structural alphabet for proteins, in: J. Mol. Biol., 2004, pp. 591-605.
• 28M. L. Connolly.
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• 29R. Dunbrack.
  Rotamer libraries in the 21st century, in: Curr Opin Struct Biol, 2002, vol. 12, n^o 4, pp. 431-440.
• 30A. 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.
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  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.
• 33H. Gohlke, G. Klebe.
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• 34J. 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.
• 35V. 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.
• 36E. 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.
• 37I. 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.
• 38J. 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.
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  Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics, Springer, 2007.
• 40E. 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.
• 41D. Rajamani, S. Thiel, S. Vajda, C. Camacho.
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• 42D. Reichmann, O. Rahat, S. Albeck, R. Meged, O. Dym, G. Schreiber.
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• 44G. Rylance, R. Johnston, Y. Matsunaga, C.-B. Li, A. Baba, T. Komatsuzaki.
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• 45G. Schreiber, L. Serrano.
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• 46M. Sippl.
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• 47C. 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.
• 48S. Wodak, J. Janin.
  Structural basis of macromolecular recognition, in: Adv. in protein chemistry, 2002, vol. 61, pp. 9–73.