Charles Robert

*The HAL version of this CV (at bottom of page) is in progress and includes links to some full-text articles. But many entries are missing or doubled.* *La version HAL de ce CV (en bas de la page) est en progrès et contient des liens vers la version en texte intégral de certains articles. Mais plusieurs publications manquent, et d'autres sont en double.* ### CNRS Laboratoire de Biochimie Théorique #### Institut de Biologie Physico-Chimique, Paris ### Diplômes 2007 HDR Sciences de la Vie, Université Paris Sud 11, Orsay FRANCE 1988 PhD (Doctor of Philosophy) en Chimie, University of Colorado, Boulder, (USA) 1982 BA (Bachelor of Arts) en Chimie, The Colorado College, Colorado Springs (USA) ### Prix et Distinctions Directeur de Recherche CNRS (DR2, 2012) Fellow de la Fondation Guggenheim (1994) ### Parcours Professionnel 2009-présent CNRS Laboratoire de Biochimie Théorique, IBPC Paris 1999-2009 CNRS IBBMC Orsay, IBPC Paris Paris, Gif-sur-Yvette 1994-1999 Chercheur Associé, Paris, Gif-sur-Yvette 1992-1994 Professeur Assistant de Recherche, Oregon State University (USA) 1990-1991 Chercheur postdoctoral, Oregon State University (USA) 1988-1990 Chercheur postdoctoral, Université de Bâle (Suisse) 1982-1988 Ph.D. en Chimie, University of Colorado, Boulder (USA) 1981-1982 Assistant de recherche, The Colorado College (USA) ### Recherche Approches théoriques des systèmes macromoléculaires en biologie Structure et dynamique des protéines et de leurs interactions ### Enseignement > 250 h aux USA et en France de 1983 à 2020 aux niveaux License, Master, Ph.D., et formation continue ### Research Articles #### 50 research articles in peer-reviewed journals 50\. C. H. Robert (2020). “\[Rp\] ReScience ten-year reproducibility challenge: estimating friction coefficients of mixed globular/chain molecules, such as protein/DNA complexes" ReScience C 6 (1), 4, 1-9. 49\. Laurin, Y., J. Eyer, C. H. Robert, C. Prévost, S. Sacquin-Mora (2017). “Mobility and core-protein binding patterns of disordered C-terminal tails in β-tubulin isotypes” Biochemistry 56 (12), 1746–1756. 48\. Roth CA, Dreyfus T, Robert CH\* and Cazals F\*. (2016) "Hybridizing rapidly growing random trees and basin hopping yields an improved exploration of energy landscapes" J. Comput. Chem. 37, 739-752. \[\*Corresponding authors CH Robert and F Cazals.\] 47\. D Chakravarty, J Janin, CH Robert and P Chakrabarti (2015) "Changes in protein structure at the interface accompanying complex formation." Intl. Union Crystallography J. 2 (6), 643-652. \[F1000Prime Recommended. Subject of an editorial article by Laskowski & Thornton in the same issue.\] 46\. Y. Laurin, P. Savarin, CH Robert, M Takahashi, J Eyer, C Prévost and S Sacquin-Mora (2015) "Investigating the structural variability and binding modes of the glioma targeting NFL-TBS.40-63 peptide on tubulin." Biochemistry 54, 3660-9. 45\. F Cazals, T Dreyfus, D Mazauric, A Roth, and CH Robert (2015) "Conformational ensembles and sampled landscapes: analysis and comparison" J. Comput. Chem. 36, 1213-31. 44\. B Boyer, J Ezelin, P Poulain, A Saladin, M Zacharias, CH Robert & C Prévost (2015) "An Integrative Approach to the Study of Filamentous Oligomeric Assemblies, with Application to RecA." PLoS ONE 10(3): e0116414. doi: 10.1371/journal.pone.0116414. 43\. Chakravarty, D, Guharoy M, Robert CH, Chakrabarti P, and Janin J. (2013) "Reassessing buried surface areas in protein-protein complexes" Protein Science 22, 1453-57. 42\. Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovalı SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Patapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, and Baker D. (2011) "Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology" J Mol Biol 414 (Nov.), 289-302. 41\. Batista PR, Pandey, G, Bisch PM, Pascutti PG, Perahia, D\* & Robert CH\* (2011) "Free energy profiles along consensus normal modes provide insight into HIV-1 protease flap opening" J Chem Theory Comput 7, 2348–52. \[\*Corresponding authors D Perahia and CH Robert\] 40\. Costa, MGS, Batista PR, Shida CS, Robert CH, Bisch PM & Pascutti PG (2010) "How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics" BMC Genomics 11, S5. 39\. Guharoy M, Janin J & Robert CH (2010) "Side-chain rotamer transitions at protein-protein interfaces" Proteins: Struct, Funct and Bioinformatics 78, 3219-25 38\. Ben Hamida-Rebaï M & Robert CH (2010) "A computational study of a recreated G protein-GEF reaction intermediate competent for nucleotide exchange: fate of the Mg ion" PLoS ONE, 5, 2, e9142 37\. Batista PR, Robert CH, Maréchal JD, Ben Hamida-Rebaï M, Pascutti PG, Bisch PM & Perahia D (2010) "Consensus Modes, a robust description of protein collective motions from multiple-minima normal mode analysis" Phys Chem Chem Phys 12, 2850-59. 36\. Drevelle A., Urvoas A., Ben Hamida-Rebaï M., Van Vooren G., Nicaise M., Valerio M., Desmadril M., Robert C. H. & Minard P., (2009) "Disulfide bond substitution by directed evolution in an engineered protein binding scaffold" ChemBioChem 10, 1349-59. 35\. Adkins NL, McBryant SJ, Johnson CN, Leidy JM, Woodcock CL, Robert CH, Hansen JC, Georgel PT (2009) "Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers", Biochemistry 48, 276-88. 34\. Hajjar E, Perahia D, Débat H, Nespoulous C & Robert CH (2006) "Odorant Binding and Conformational Dynamics in the Odorant-binding Protein", J Biol Chem 281, 29929-29937. 33\. Floquet N., Marechal J., Badet-Denisot M., Robert CH, Dauchez M & Perahia D (2006) "Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors", FEBS Lett, 2006, 580, 5130-5136. 32\. Robert, C. H., Cherfils, J., Mouawad, L., and Perahia, D. (2004) "Integrating three views of Arf1 activation dynamics", J Mol Biol 337, 969-983. 31\. Georgel P and Robert CH (2002) "Differential core histone binding behavior: RNA polymerase I promoter region vs. 5S rDNA positioning DNA sequences" Cell Biochem Biophys 37, 1-13. 30\. Mouawad L, Perahia D, Robert CH, and Guilbert C. (2002) "New insights into the allosteric mechanism of human hemoglobin from molecular dynamics simulations" Biophys J. 82, 3224–3245. 29\. Robert, C. H., and Janin, J. (1998) "A soft, mean-field potential derived from crystal contacts for prediction of protein-protein interactions" J. Mol. Biol. 283, 1037-1047. 28\. Gabb, H. A., Prévost, C., Bertucat, G., Robert, C. H., and Lavery, R. (1997) "Collective-variable Monte Carlo simulation of DNA" J. Comp. Chem. 18, 2001-2011. 27\. Gabb, H., Sanghani, S., Robert, C. H., and Prévost, C. (1996) "Finding and visualizing nucleic acid base stacking" J. Mol. Graphics. 14, 6-11. 26\. Robert, C. H. "Estimating friction coefficients of mixed globular/chain molecules, such as protein/DNA complexes" (1995) Biophysical J. 69, 840-848. 25\. Robert, C. H., and Ho, P. S. (1995) "Significance of bound water to local chain conformations in protein crystals" Proc. Natl. Acad. Sci. USA 92, 7600-7604. 24\. Leuba, S. H., Yang, G., Robert, C., Samori, B., van Holde, K., Zlatanova, J., and Bustamante, C. (1994) "Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy" Proc. Natl. Acad. Sci. (USA) 91, 11621-11625. 23\. van Holde, K. E., Lohr, D. E., and Robert, C. (1992) "What happens to nucleosomes during transcription?" J. Biol. Chem. 267, 2837-2840. 22\. Schwarz, G. and Robert, C. H. (1992) "Kinetics of pore-mediated release of marker molecules from liposomes or cells" Biophys. Chem. 42, 291-296. 21\. Stankowski, S., Pawlak, M., Kaisheva, E., Robert, C.H., and Schwarz, G. (1991) "A combined study of aggregation, membrane affinity, and pore activity of natural and modified melittin" Biochim. Biophys. Acta 1069 77-86. 20\. Robert, C. H. (1990) "A hierarchical 'nesting' approach to describing the stability of alpha-helices with side-chain interactions" Biopolymers 30, 335-347. 19\. Schwarz, G. and Robert, C. H. (1990) "Pore formation kinetics in membranes, determined from the release of marker molecules out of liposomes or cells." Biophys. J. 58, 577-583. 18\. Gill, S. J., Murphy, K. P., and Robert, C. H. (1990) "Partition function formalism for analyzing calorimetric experiments" J. Chem. Ed. 67, 928-931. 17\. Robert, C. H., Colosimo, A., and Gill, S. J. (1989) "Allosteric formulation of thermal transitions in biological macromolecules, including effects of ligand binding and oligomerization" Biopolymers 28, 1705-1729. 16\. Connelly, P. R., Johnson, C., Robert, C. H., Beintima, J., and Gill, S. J. (1989) "Binding of oxygen and carbon monoxide to the hemocyanin from the spiny lobster" J. Mol. Biol. 207, 829-832. 15\. Gill, S. J., Di Cera, E., Doyle, M. L., and Robert, C. H. (1988) "New twists on an old story: hemoglobin" Trends Biochem. Sciences 13, 465-467 \[review article\]. 14\. Robert, C. H., Fall, L., and Gill, S. J. (1988) "Linkage of organic phosphates to oxygen binding in human hemoglobin at high concentrations" Biochemistry 27 6835-6843. 13\. Robert, C. H., Gill, S. J., and Wyman, J. (1988) "Quantitative evaluation of linkage in macromolecules when one ligand is present in limited total amount" Biochemistry 27 6829-6835. 12\. Decker, H., Connelly, P. R., Robert, C. H., and Gill, S. J. (1988) "Nested allosteric interaction in tarantula hemocyanin revealed through the binding of carbon monoxide" Biochemistry 27 6901-6908. 11\. Gill, S. J., Connelly, P. R., Di Cera, E., and Robert, C. H. (1988) "Analysis and parameter resolution in highly cooperative systems" Biophys. Chem. 30 133-141. 10\. Hallen, D., Wadso, I., Wasserman, D. J., Robert, C. H., and Gill, S. J. (1988) "Enthalpy of dimerization of benzene in water" J. Phys. Chem. 92 3623-3625. 9\. Robert, C. H., Decker, H., Richey, B., Gill, S. J., and Wyman, J. (1987) "Nesting: Hierarchies of allosteric interaction" Proc. Natl. Acad. Sci. USA 84 1891-1895. 8\. Doyle, M. L., Di Cera, E., Robert, C. H., and Gill, S. J. (1987) "Carbon dioxide and oxygen linkage in human hemoglobin tetramers" J. Mol. Biol. 196 927-934. 7\. Parody-Morreale, A., Robert, C. H., Bishop, G. A., and Gill, S. J. (1987) "Calorimetric studies on the binding of oxygen and carbon monoxide to human hemoglobin HbAo: Sequential binding heats for oxygen" J. Biol. Chem. 23 10994-10999. 6\. Di Cera, E., Robert, C. H., and Gill, S. J. (1987) "Allosteric interpretation of the oxygen binding reaction of human hemoglobin tetramers" Biochemistry 26 4003-4008. 5\. Gill, S. J., Di Cera, E., Doyle, M. L., Bishop, G. A., and Robert, C. H. (1987) "Oxygen binding constants for human hemoglobin tetramers" Biochemistry 26 3995-4002. 4\. Bishop, G. A., Parody-Morreale, A., Robert, C.H., and Gill, S. J. (1987) "Gas-solution microcalorimeter for determining heat binding curves" Rev. Sci. Instr. 58 632-638. 3\. Gill, S. J., Robert, C. H., Coletta, M., Di Cera, E., and Brunori, M. (1986) "Cooperative free energies for nested allosteric models as applied to human hemoglobin" Biophys. J. 50 747-752. 2\. Connelly, P. R., Robert, C. H., Briggs, W. E., and Gill, S. J. (1986) "Analysis of zeros of binding polynomials for tetrameric hemoglobins" Biophys. Chem. 24 295-309. 1\. Huebert, B. A. and Robert, C. H. (1985) "Dry deposition of nitric acid to grass" J. Geophys. Res. 90 2085-2090. ### Tech Reports 1t F. Cazals, C. Mueller, C. Robert, and A. Roth (2013) "Towards Morse theory for point cloud data." INRIA Tech Report 8331, pp 37. ### Book Chapters 6b. Cazals, F., Dreyfus, M., and Robert, C. H. (2013) "Modeling macromolecular complexes : a journey across scales". In (F. Cazals and P. Kornprobst, eds.) Modeling in Computational Biology and Biophysics, Springer Heidelberg, pp. 3-45. 5b. Miteva, M.A., Robert, C.H., Maréchal, J.D., Perahia, D. (2011) "Receptor flexibility in ligand docking and virtual screening". In (M.Miteva, ed.) In silico lead discovery, Bentham Science Publishers, pp. 99-117. 4b. Leuba, S. H., Yang, G., Robert, C., van Holde, K., Zlatanova, J. and C. Bustamante (1995) "Extended chromatin fibers: evidence from scanning force microscopy studies" SPIE Proc. 2384, 33-44. 3b. Gill, S. J., Robert, C. H., and Wyman, J., "Analysis of allosteric systems" in Biochemical Thermodynamics, 2nd Ed., M. N. Jones, ed. (Elsevier, Holland, 1988). 2b. Decker, H., Robert, C. H., and Gill, S. J., "Nesting-- An extension of the MWC model and its application to tarantula hemocyanin" in Invertebrate Oxygen Carriers, B. Linzen, ed. (Springer-Verlag, Berlin, 1987) pp.383-388. 1b. Parody-Morreale, A., Robert, C. H., and Gill, S. J., "Calorimetric analysis of oxygen binding to lobster hemocyanin" in Invertebrate Oxygen Carriers, B. Linzen, ed. (Springer-Verlag, Berlin, 1987) pp.389-393. Incomplete HAL version of this CV: ===================================