Publications

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Book Chapter
Saladin A, Prévost C.  2010.  Protein-Protein Docking. Protein-Protein Complexes. Analysis, Modeling and Drug Design. :147–181.
Journal Article
Bastard K, Prevost C, Zacharias M.  2006.  Accounting for loop flexibility during protein-protein docking. Proteins. 62:956–969.
Zhu S, Stroebel D, C Yao A, Taly A, Paoletti P.  2013.  Allosteric signaling and dynamics of the clamshell-like NMDA receptor GluN1 N-terminal domain. Nature Structural \& Molecular Biology. 20:477–485.
Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete N-V, Cote S, De Simone A, Doig AJ, Faller P, Garcia A et al..  2015.  Amyloid beta Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev.. 115:3518–3563.
Yun MR, Lavery R, Mousseau N, Zakrzewska K, Derreumaux P.  2006.  ARTIST: An activated method in internal coordinate space for sampling protein energy landscapes. Proteins: Struct., Funct., Bioinf.. 63:967–975.
Zhang T, Xu W, Mu Y, Derreumaux P.  2014.  Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-L-tryptophan Inhibitor on Alzheimer's A beta 1-42 Dimer in Terms of Aggregation and Toxicity. Acs Chem. Neurosci.. 5:148–159.
Schneider S., Saladin A, Fiorucci S., Prevost C., Zacharias M.s.  2012.  ATTRACT and PTOOLS: Open source programs for protein-protein docking. Methods Mol. Biol.. 819:221–232.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Fleishman SJ, Whitehead TA, Strauch E-M, Corn JE, Qin S, Zhou H-X, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G et al..  2011.  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.. J. Mol. Biol.. 414:289–302.
Katava M, Stirnemann G, Zanatta M, Capaccioli S, Pachetti M, Ngai KL, Sterpone F, Paciaroni A.  2017.  Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion. Proc Natl Acad Sci U S A. 114:9361-9366.
Zhang T, Nguyen PH, Nasica-Labouze J, Mu Y, Derreumaux P.  2015.  Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J. Phys. Chem. B. 119:6941–6951.
Qiu Y, Zhao Y, Becker M, John S, Parekh BS, Huang S, Hendarwanto A, Martinez ED, Chen Y, Lu H et al..  2006.  HDAC1 acetylation is linked to progressive modulation of steroid receptor-induced gene transcription.. Mol. Cell. 22:669–679.
Ziolkowska K, Derreumaux P, Folichon M, Pellegrini O, Regnier P, , Hajnsdorf E.  2006.  Hfq variant with altered RNA binding functions. Nucleic Acids Res.. 34:709–720.
Stirnemann G, Kang S-gu, Zhou R, Berne BJ.  2014.  How force unfolding differs from chemical denaturation.. Proc. Natl. Acad. Sci. U.s.a. 111:3413–8.
Boyer B, Ezelin J, Poulain P, Saladin A, Zacharias M, Robert CH, Prévost C.  2015.  An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. Plos One. in press:e0116414.
Xu W, Zhang C, Derreumaux P, Graslund A, Morozova-Roche L, Mu Y.  2011.  Intrinsic Determinants of A beta(12-24) pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies. Plos One. 6:e24329.
Saladin A, Amourda C., Poulain P., Ferey N., Baaden M., Zacharias M., Delalande O., Prevost C..  2010.  Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments. Nucleic Acids Res.. 38:6313–6323.
Zhang T, Zhang J, Derreumaux P, Mu Y.  2013.  Molecular Mechanism of the Inhibition of EGCG on the Alzheimer A beta(1-42) Dimer. J. Phys. Chem. B. 117:3993–4002.
Zhang T, Zhang J, Derreumaux P, Mu Y.  2013.  Molecular Mechanism of the Inhibition of EGCG on the Alzheimer A beta(1-42) Dimer. J. Phys. Chem. B. 117:3993–4002.
Kamashev D, Oberto J, Serebryakova M, Gorbachev A, Zhukova Y, Levitsk, ii S, Mazur AK, Govorun V.  2011.  Mycoplasma gallisepticum produces a histone-like protein that recognizes base mismatches in DNA. Biochemistry. 50:8692–8702.
Saladin A, Fiorucci S, Poulain P, Prevost C, Zacharias M.  2009.  PTools: an opensource molecular docking library.. Bmc Struct. Biol.. 9:27–37.

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