Chapitres de livre

-   Biologie structurale et géométrie.
M.A. Delsuc, T.E. Malliavin, A. Marin, B. Mourrain
Collection La Science au Présent. Encyclopedia Universalis (2007)

-   DNA/protein modeling.
R. Lavery
dans Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Section editor W.R. Taylor, Wiley, (2004).

-   DNA structure, dynamics and recognition.
R. Lavery
dans Multiple Aspects of DNA and RNA from Biophysics to Bioinformatics, ed. D. Chatenay et al., Elsevier (2005).

-   Modeling DNA deformation.
P. Varnai, R. Lavery
dans Computational Studies of DNA and RNA, F. Lankas et J. Sponer (eds.) Springer Verlag (2006) 169-210

-   Exploring the folding and aggregation mechanisms of amyloid-forming peptides by computer simulations
S. Santini, G. Wei, N. Mousseau, P. Derreumaux,
Life Sciences/CRC Press, Amyloid and Amyloidosis: from molecular dissection to therapeutics, G. Grateau , R. Kyle, M. Skinner Editors, p. 200-203 (2005).

-   Prion protein. Amyloid proteins: the beta sheet conformation and disease
P. Derreumaux
J. Sipe (Ed.), Wiley-VCH Verlag GmbH, 2: 493-513 (2005).

 2006

• T.lionnet, S.Joubaud, R.Lavery,D. Bensimon, V.Croquette (2006) "Wringing out DNA". Phys. Rev. Lett. 96 178102.

• R.Lavery Q. Rev."Recognizing DNA."  Biophys. 38 (2005) 339-344.

• F. Lankas, R. Lavery, J.H. Maddocks (2006)"DNA kinking occurs during molecular dynamics simulations of small minicircles." Structure  14 1527-1534.

• F. Cailliez, R. Lavery (2006) "Dynamics and stability of E-cadherin dimers".  Biophys.J. 91 3964-3971.

• Timsit Y, Allemand F, Chiaruttini C, Springer M. (2006) "Coexistence of two protein folding states in the crystal structure of ribosomal protein L20." EMBO Rep.;7(10):1013-8.

• Gelly JC, Etchebest C, Hazout S, de Brevern AG. (2006)  "Protein Peeling 2: a web server to convert protein structures into series of protein units." Nucleic Acids Res. Jul 1;34(Web Server issue):W75-8.

• Gelly JC, de Brevern AG, Hazout S. (2006) 'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments. Bioinformatics. Jan 15;22(2):129-33. Epub 2005 Nov 14.

• T.E. Malliavin (2006) "Quantitative analysis of biomolecular NMR spectra: a prerequisite for the determination of the structure and dynamics of biomolecules." Current Organic Chemistry 10, 555-568.

• B. Bardiaux, T.E. Malliavin, M. Nilges, A.K. Mazur (2006) "Comparison of different torsion angle approaches for NMR structure determination." J. Biomol. NMR 34, 153-156.

• W. Rieping, M. Habeck, B. Bardiaux, T. E. Malliavin, A. Bernard, M. Nilges ARIA2: "Automated NOE assignment and data integration in NMR structure calculation". Bioinformatics, sous presse.

• F. Joli F., N. Bouchemal, E. Hantz, B. Hartmann (2006) "NMR and molecular modelling studies of an RNA hairpin containing a G-rich hexaloop." CRAS 9, 426-432.

• F. Joli, E. Hantz, B. Hartmann (2006) "Structure and dynamics of phosphate linkages and sugars in an abasic hexaloop RNA hairpin." Biophys. J.  90, 1480-1488.

• B. Heddi, N. Foloppe, N. Bouchemal, E. Hantz, B. Hartmann (2006) "Quantification of DNA BI/BII backbone sub-states in solution. Implications for DNA overall structure and recognition." JACS 128, 9170-9177.

• F. Joli F., N. Bouchemal, A. Laigle, B. Hartmann, E. Hantz (2006) "Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides." Nuc. Acids Res., in press.

• A. K. Mazur Evaluation of elastic properties of atomistic DNA models (2006) Biophys. J., 91, in press.

• I. Brovchenko, A. Krukau, A. Oleinikova, A. K. Mazur (2006) "Water percolation governs polymorphic transitions and conductivity of DNA"  Phys. Rev. Lett., 97, 137801.  

• B. Bardiaux, T. E. Malliavin, M. Nilges, A. K. Mazur (2006) "Comparison of different torsion angle approaches for NMR structure termination " J. Biol. NMR, 34, 153-166.

• S. Zirah, S. A. Kozin, A. K. Mazur, A. Blond, M. Cheminant, I.  Ségalas-Milazzo, P. Debey and S. Rebuffat (2006) "Structural changes of region 1-16 of the Alzheimer disease amyloid beta-peptide upon zinc binding and in vitro aging"  J. Biol. Chem., 281, 2151-2161.

• K. Tai, M. Baaden, S. Murdock, B. Wu, M. Hong Ng, S. Johnston, J.W. Essex, M.S.P. Sansom (2006) "Three hydrolases and a transferase: Comparative analysis of active-site dynamics via the BioSimGrid database". J.Mol.Graph.Model., (publié en ligne Sept. 2006)

• K. Cox, P.J. Bond, A. Grottesi, M. Baaden, M.S.P. Sansom (2006) "Outer membrane proteins: comparing X-Ray and NMR structures by MD simulations in lipid bilayers." Eur. Biop. J. (accepté)

• M-R. Yun, R. Lavery, N. Mousseau, K. Zakrzewska, P. Derreumaux, "ARTIST: an activated method in internal coordinate space for sampling protein energy landscapes." Proteins Structure Genetics Bioinformatics, 63 : 967-75 (2006).

• K. Ziolkowska, P. Derreumaux, M. Folichon, O. Pellegrini, P. Regnier, I.V. Boni,  E. Hajnsdorf, "A missense mutation in the Sm1 domain of Hfq Ec affects binding to polyadenylated RNA, poly(A) synthesis stimulation, rpoS expression and autocontrol of Hfq synthesis." Nucleic Acids Research,  34: 709-720  (2006).

• G. Boucher, N. Mousseau, P. Derreumaux, "Aggregating the Alzheimer's Abeta{11-25} peptide into a four-stranded beta-sheet structure", Proteins, in press (2006).

• A. Melquiond, N. Mousseau, P. Derreumaux, (2006)."Structure of soluble amyloid oligomers from computer simulations". Proteins Structure Genetics Bioinformatics, 65 : 180-191 

• W. Chen, P. Derreumaux, N. Mousseau, (2006) "The conformations of the Amyloid-beta(21-30) fragment can be described by three families in solution", J. Chem. Phys. 125(8) : 084911

• A. Huet, P. Derreumaux, (2006) "Impact of the mutation A21G (Flemish variant) on Alzheimer's beta-Amyloid dimers by molecular dynamics simulations", Biophys. J., 91 :3829-40  .

• P. Derreumaux, N. Mousseau, Coarse-grained protein molecular dynamics simulations, J. Chem. Phys. in press (2006)

• B.Datta, G.B.Schuster, A.McCook, S.Harvey, K.Zakrzewska "DNA-Directed Assembly of Polyanilines: Modified Cytosine Nucleotides Transfer Sequence Programmability to a Conjoined Polymer", J. Am. Chem. Soc. sous presse.

• Bastard K, Prevost C, Zacharias M. (2006) Accounting for loop flexibility during protein-protein docking. Proteins. Mar 1;62(4):956-69.

2005

• R. A. O’Flanagan, G. Paillard, A. M. Sengupta, R. Lavery (2005) "Non-additivity in protein-DNA binding." Bioinformatics 21, 2254-2263.

• C. Deremble, R. Lavery (2005) "Macromolecular recognition". Curr. Opin. Struct. Bio. 15, 171-175.

• S.B. Dixit, D.L. Beveridge, D.A. Case, T.E. Cheatham III, E. Giudice, F. Lankas, R. Lavery, J.H. Maddocks, R. Osman, H. Sklenar, K.M. Thayer, P. Varnai (2005) "Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II. Sequence context effects on the dynamical structures of the 10 unique Dinucleotide Steps." Biophys. J. 89, 3721-3740.

• F. Cailliez, R. Lavery (2005) "Cadherin mechanics and complexation: the importance of calcium binding." Biophys. J. 89, 3895-3903.

• Djuranovic, B. Hartmann (2005) "Molecular dynamics studies on free and bound targets of the BPV-1 E2 protein : the protein binding effect on DNA and the recognition mechanism". Biophys. J. 89, 2542-2551.

• A. K. Mazur "Electrostatic polymer condensation and the A/B polymorphism in DNA". (2005) J. Biomol. Struct. Dyn., 22, 792.

• D. E. Kamashev and A. K. Mazur (2005) "Compressed backbone hypothesis of B-DNA fine structure and dynamics". J. Biomol. Struct. Dyn. 22, 777-778.

• A. K. Mazur "Electrostatic polymer condensation and the A/B polymorphism  in DNA: Sequence effects" (2005) J. Chem. Theory. Comp., 1, 325-336.

• R.J. Law, C.E. Capener, P.J. Bond, M. Baaden, G. Patargias, J. Campbell, Y. Pathy, M.S.P. Sansom (2005) "Relationship of protein structure quality with stability and mechanistic determination in Molecular Dynamics simulation of membrane proteins." J.Mol.Graph.Model., 24, 157-165

• P. Tuffery, F. Guyon, P. Derreumaux (2005). "An improved greedy algorithm for protein structure reconstruction", J. Comput. Chem. 26: 506-513

• M. Coincon, A. Heitz, L. Chiche, P. Derreumaux, (2005). "The BABAB elementary  supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule". Proteins: Structure, Function and Bioinformatics, 60, 740-745

• A. Melquiond, G. Boucher, N. Mousseau, P. Derreumaux, (2005)."Following the aggregation of amyloid-forming peptides by computer simulations." J. Chem. Phys., 122, 174904

• P. Tuffery, P. Derreumaux, (2005) "Dependency between consecutive local conformations helps assemble  protein structures from secondary structures using Go potential and greedy algorithm" Proteins: Structure, Function and Bioinformatics, 61: 732-740

• N. Mousseau, P. Derreumaux, G. Gilbert (2005)."Analysis of the energy landscape of small proteins using the activation-relaxation technique". Physical Biology, 2 :S101-7

• N. Mousseau, P. Derreumaux (2005)."Exploring the early steps of amyloid peptide aggregation by computers." Acc. Chem. Res., 38, 885-891

• Emanuele E., Markovitsi D., Millie P., Zakrzewska K. (2005) "UV Spectra and Excitation Delocalization in DNA: Influence of the Spectral Width.” Chem.Phys.Chem., 6, 1387-1392.

• Emanuele E., Zakrzewska K., Markovitsi D., Lavery R., Millie P. (2005) "Exciton states of dynamic DNA double helices: alternating dCdG sequences". J. Phys. Chem. Β, 109, 16109 -16118

2004

• I. Navizet, R. Lavery, R.L. Jernigan (2004) “Myosin flexibility: structural domains and collective vibrations” Proteins 54, 384-393.

• G. Paillard, R. Lavery (2004) “Analyzing Protein-DNA recognition mechanisms”. Structure 12, 113-122.

• I. Navizet, F. Cailliez, R. Lavery (2004) “Probing protein mechanics: residue level properties and their use in defining domains”. Biophys. J. 87, 1426-1435.

• D.L. Beveridge, D.A. Case, T.E. Cheatham III, S. Dixit, E. Giudice, F. Lankas, R. Lavery, J.H. Maddocks, R. Osman, H. Sklenar, G. Stoll, K. Thayer, P. Várnai, M.A. Young (2004) “Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design, informatics and results on CpG steps”. Biophys. J. 87, 3799-3813.

• G. Paillard, C. Deremble, R. Lavery (2004) “Looking into DNA recognition: Zinc-finger binding”. Nucleic Acids Res. 32, 6673-6682.

• M. Canalia, T.E. Malliavin, W. Kremer, H.R. Kalbitzer (2004)  “Molecular dynamics simulations of HPr under hydrostatic pressure.” Biopolymers 74, 377-388.

• A. Marin, T.E. Malliavin, P. Nicolas, M.A. Delsuc (2004) “From NMR chemical shifts to amino acid types: investigation of the predictive power carried by nuclei.” J. Biomolec. NMR 30, 47-60.

• J.L. Pons, T.E. Malliavin, D. Tramesel, M.A. Delsuc (2004) “NMRb : A Web-repository for raw NMR data-sets.” Bioinformatics 20, 3707-3709.

• S. Telechea, B. Hartmann, J. Kozelka (2004) “Three interproton distances define the BI and BII backbone sub-states in the B-DNA.” J. Biomol. Struct. Dyn. 21, 489-494.

• D. Djuranovic, B. Hartmann (2004) “DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations”. Biopolymers 73, 356-368.

• Djuranovic, C. Oguey, B. Hartmann (2004) “The role of DNA structure and dynamics in the recognition of bovine papillomavirus E2 protein target sequences”. J. Mol. Biol. 339, 785-796

• K.Mazur, S. N. Kovalchuk, E. V. Agafonova, V. V. Sova, L. A. Elyakova and V.A. Rasskazov (2004) “Molecular cloning of a mollusk glucanase” Comp. Biochem. Physiol., 137, 169-178.

• D. E. Kamashev and A. K. Mazur (2004) “Single-stranded breaks relax intrinsic curvature in DNA?” Biochemistry, 437, 8160-8168.

• J.D. Faraldo−Gómez, L.R. Forrest, M. Baaden, P.J. Bond, C. Domene, G. Patargias, J. Cuthbertson, M.S.P. Sansom (2004) “Conformational sampling and dynamics of membrane proteins from 10−nanosecond computer simulations”. Proteins, 57, 783-791

• Baaden, M.S.P. Sansom (2004) “OMPT: Molecular Dynamics simulations of an outer membrane enzyme”. Biophys. J., 87, 2942-2953

• N. Floquet, S. Pasco, L. Ramont, P. Derreumaux, J-Y. Laronze, J-M. Nuzillard, F.X. Maquart, A.J.P Alix, J-C. Monboisse, (2004). “The anti-tumor properties of the alpha3 (IV) 185-203 peptide from the NC1 domain of type IV collagen (Tumstatin) are conformation-dependent.” J. Biol. Chem. 279: 2091-2100 

• N. Floquet, S. Hery-Huynh, M. Dauchez, P. Derreumaux, A.M. Tamburo, A.J.P. Alix, (2004) “Structural characterization of VGVAPG, an elastin derived peptide”.  Biopolymers 76: 266-280.

• G. Wei, N. Mousseau, P. Derreumaux, (2004).“Complex folding pathways in a beta-hairpin.” Proteins 56: 464-474

• S. Santini, P. Derreumaux, (2004). “The helix H1 of the prion protein is rather stable against environmental perturbations:  molecular dynamics of mutation and deletion variants of PrP (90-231).” Cellular and Molecular Life Sciences 61: 951-60

• Arluison, M. Folichon, S. Marco, P. Derreumaux, O. Pellegrini, E. Hajnsdorf, P. Regnier, (2004).”The C-terminal domain of E. coli Sm-like Hfq  is implicated in protein stability, not in RNA binding.” Eur. J. Biochemistry 271: 1258-65

• S. Santini, G. Wei, N. Mousseau, P. Derreumaux, (2004) "Pathway complexity of Alzheimer's beta-amyloid Abeta{16-22} peptide assembly". Structure 12: 1245-55

• S. Santini, N. Mousseau, P. Derreumaux, (2004). "In silico assembly of Alzheimer's Abeta{16-22} peptide into beta-sheets". J. Am. Chem. Soc. 126: 11509-11516

• G. Wei, N. Mousseau, P. Derreumaux, (2004)."Sampling the self-assembly pathways of KFFE hexamers", Biophys. J. 87: 3648-56

• G. Wei, N. Mousseau, P. Derreumaux, (2004) "Assembly dynamics of KFFE octamers", J. Phys. Condensed Matter 16: 5047-5054

• Sun B-W, Babu B.R., Sørensen M.D.,Zakrzewska K., Wengel J., Sun J-S, (2004) “Sequence and pH Effects of LNA-Containing Triple Helix-Forming Oligonucleotides: Physical Chemistry, Biochemistry and Modelling Studies" Biochemistry,43, 4160 -4169

•  Varnai P., Zakrzewska K. (2004) "DNA and its counterions: a molecular dynamics study", Nuc Acids Res, 32, 4269-4280

• Chrowos A., Arnaud P., Zakrzewska K., Guga P., Pratviel G., Stec W., Meunier B.,(2004) " Comparison of the cleavage profiles of nucleotide duplexes with or without phosphorothioate linkages by using a chemical nuclease probe", J.Biol Inorg Chem ,9,374-384.

• Selmane T, Camadro JM, Conilleau S, Fleury F, Tran V, Prevost C, Takahashi M., (2004) "Identification of the subunit-subunit interface of Xenopus Rad51.1 protein: similarity to RecA." J Mol Biol. Jan 23;335(4):895-904.

 2003

• E. Giudice, P. Várnai, R. Lavery (2003) “Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations”. . Nucleic Acids Res. 31, 1434-1443.

• E. Giudice, R. Lavery (2003) “Nucleic acid base pair dynamics: the impact of sequence and structure using free energy calculations”. J. Am. Chem. Soc. 125, 4998-4999.

• K. Bastard, A. Thureau, R. Lavery, C. Prévost (2003) “Docking macromolecules with flexible segments”. J. Comp. Chem. 30, 1910-1920.

• B. Hartmann, M.R. Sullivan, L.F. Harris (2003) “Operator recognition by the phage 434 cI repressor: MD simulations of free and bound 50bp DNA reveal important differences between OR1 and OR2 sites”. Biopolymers 68, 250-264.

• Djuranovic, B. Hartmann (2003) “Conformational characteristics and correlations in crystal structure of nucleic acid oligonucleotides: evidence of sub-states”. J. Biomol Struct Dyn. 20, 771-788.

• A. K. Mazur (2003) “Titration in silico of reversible B<->A transitions in DNA” J. Am. Chem. Soc.,125, 7849-7859.

• Baaden, F. Berny, R. Schurhammer, C. Madic, G. Wipff (2003) “Theoretical studies on lanthanide cation extraction by picolinamides: ligand-cation interactions and interfacial behavior”. Solv. Extr. Ion Exch., 21, 199-219

• J. D. Campbell, P. C. Biggin, M. Baaden, M.S.P. Sansom (2003) “Extending the structure of an ABC transporter to atomic resolution: modelling and simulation studies of Msba”. Biochemistry, 42, 3666-3673

• Baaden, C. Meier, M.S.P. Sansom (2003) “A molecular dynamics investigation of mono- and dimeric states of the outer membrane enzyme Ompla”. J. Mol. Biol., 331, 177-189

• S. Santini, J-B. Claude, S. Audic, P. Derreumaux, (2003).”Impact of the tail and mutations G131V and M129V on prion protein flexibility”. Proteins 51: 258-265

• N. Gresh, P. Derreumaux, (2003) “Generating conformations for two zinc binding sites of HIV-1 nucleocapsid protein from random conformations by a hierarchical procedure and polarizable force field”. J. Phys. Chem. B 107:4862-4870

• P. Derreumaux, (2003) “Role of supersecondary structural elements in protein G folding”. J. Chem. Phys. 119: 4940-4944

• G. Wei, P. Derreumaux, N. Mousseau, (2003). “Sampling the complex energy landscape of a simple beta-hairpin”. J. Chem. Phys.  119: 6403-6406 

• S. Santini, G. Wei, N. Mousseau, P. Derreumaux, (2003) “Exploring the folding pathways of proteins through energy landscape sampling: Application to Alzheimer's beta-amyloid peptide”. Internet Electron. J. Mol. Des. 2: 564-577

• Gao K., Fan B.T., El Fassi N., Zakrzewska K., Jia Z., Zheng R., Panaye A., Couesnon T., Doucet J-P. "Comparative Study of Activities between Verbascoside and Rutin by Docking Method" Quant. Struct-Act. Relat, 22 (2003),1-11

• Arnaud Ph., Zakrzewska K., Meunier B., (2003) “Theoretical study of the interaction between manganese derivative of porphyrin (oxyl-Mn(IV)-TMPyP) and DNA” J.Comp. Chem, 24,797-805

• Zakrzewska K., (2003), “DNA deformation energetics and protein binding” Biopolymers 70, 414-423

• Bouvier B.,  Dognon J.P.,  Lavery R, Markovitsi D., Millié P., Onidas D., Zakrzewska K., (2003), “Influence of conformational dynamics on the exciton states of DNA oligomers “, J.Chem.Phys. 107, 13512-13522.

• Prevost C, Takahashi M. (2003) “Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination. Q” Rev Biophys; 36(4):429-53.

• Malliavin TE, Gau J, Snoussi K, Leroy JL. (2003) “Stability of the I-motif structure is related to the interactions between phosphodiester backbones.” Biophys J. Jun; 84(6):3838-47.

2002

• N. Foloppe, B. Hartmann, L. Nilsson A.D. MacKerell (2002) Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. Biophys. J. 82(3), 1554-1569.

• O. Delalande, K. Gao, B.T. Fan, K. Zakrzewska, Z. Jia, R. Zheng, N. Elfasi, A. Panaye, J.-P. Doucet (2002) Docking study of cistanoside C to telomeric DNA fragment. SAR QSAR in Environ. Res. 13, 675-688.

• E. Giudice, R. Lavery (2002) Simulations of nucleic acids and their complexes. Acc. Chem. Res. 35, 350-357.

• S.C. Harvey, C. Wang, S. Teletchea, R. Lavery (2002) Modeling structural motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking. J. Comput. Chem. 24, 1-9.

• R. Lavery, A. Lebrun, J-F. Allemand, D. Bensimon, V. Croquette (2002) Structure and mechanics of single biomolecules: experiment and simulation. J. Phys. (Cond. Mat.) 14, R383-R414.

• T.E. Malliavin, E. Giudice (2002) Analysis of peptide rotational diffusion by homonuclear NMR. Biopolymers 63, 335-342.

• A.K. Mazur, D.E. Kamashev (2002) Simulated and experimental bending dynamics in DNA with and without regularly repeated adenine tracts. Phys. Rev. E 66, 011917(1-13).

• A.K. Mazur (2002) DNA dynamics in a water drop without counterions. J. Am. Chem. Soc. 124, 14707-14715.

• O. Sperandio, B.T. Fan, K. Zakrzewska, HZ. Jia, R.L. Zheng, A. Panaye, J.P. Doucet, N. El Fassi (2002) Theoretical study of fast repair of DNA damage by cistanoside C and analogs: mechanism and docking. SAR QSAR in Environ. Res. 13, 243-260.

• P. Várnai, R. Lavery (2002) Base flipping in DNA: pathways and energetics studied using molecular dynamic simulations. J. Am. Chem. Soc. 124, 7272-7273.

• P. Várnai, D. Djuranovic, R. Lavery, B. Hartmann (2002) a/g transitions in the B-DNA backbone. Nucleic Acids Res. 30, 5398-5406.

• V. Catherinot , T.E. Malliavin, J.L. Pons, M.A. Delsuc (2002) L'attribution des spectres RMN: de l'analyse manuelle au traitement automatique. BIOforum International, édition française 2/2002, GIT Verlag.

• T.E. Malliavin (2002) Simulations de dynamique moléculaire des biomolécules à haute pression, Actes du 3^ème Forum du Réseau Hautes Pression, Collonges la Rouge.

• A.K. Mazur (2002) DNA dynamics in a water drop. Preprint physics/0204001.

2001

• M. Bykhovskaia, B. Gelmont, T. Globus, D.L. Woolard, A.C. Samuels, T. Ha-Duong, K. Zakrzewska (2001) Prediction of DNA far-IR absorption spectra based on normal mode analysis. Theoret. Chem. Accts., 106, 22-27.

• E. Giudice, P. Várnai, R. Lavery (2001) An umbrella sampling simulation of the energetic and conformational aspects of base pair opening within the DNA double helix. Chem. Phys. Chem. 2, 673-677.

• R. Gurlie, K. Zakrzewska (2001) Protein-induced DNA bending: the role of phosphate neutralization. Theoret. Chem. Accts., 106, 83-90.

• S.A. Kozin, G. Bertho, A.K. Mazur, H. Rabesona, J.-P. Girault, T. Haertle, M. Takahashi, P. Debey, G.H. Hoa (2001) Sheep prion protein synthetic peptide spanning helix 1 and beta-strand 2 (residues 142-166) shows beta-hairpin structure in solution. J. Biol. Chem. 276, 46364-46370.

• I. Lafontaine, R. Lavery (2001) High-speed molecular mechanics searches for optimal protein binding sites. Comb. Chem. High Throughput Screening 4, 707-717.

• I. Lafontaine, R. Lavery (2001) ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences. Biopolymers 56, 293-310.

• A. Lebrun, R. Lavery, H. Weinstein (2001) Modeling multi-component protein-DNA complexes: the role of bending and dimerization in the complex of p53 dimers with DNA. Protein Engineering 14, 233-243.

• T.E. Malliavin, P. Barthe, M.A. Delsuc (2001) FIRE: predicting the spatial proximity of protein residues from a 3D HSQC-NOESY. Theor. Chem. Accts 106, 91-97.

• C. Mayer, Y. Timsit (2001) Hydration and structural alteration of A-DNA. Implication for the accuracy of DNA replication. Cell Mol. Biol. 47, 815-822.

• A.K Mazur, B.G. Sumpter, D.W. Noid (2001) Internal coordinate phase space analysis of macromolecular systems. Comput. Theor. Polym. Sci. 11, 35-47.

• A.K. Mazur (2001) Molecular dynamics of minimal B-DNA. J. Comput. Chem. 22, 457-467.

• A.K. Mazur (2001) Molecular dynamics studies of sequence-directed curvature in bending locus of trypanosome kinetoplast DNA. J. Biomol. Struct. Dyn. 18, 832-843.

• Y. Timsit (2001) Convergent evolution of MutS and topoisomerase II for clamping DNA crossovers and stacked Holliday junctions. J. Biomol. Struct. Dyn. 19, 215-218.

• A.K. Mazur (2001) Internal coordinate simulation method, in Computational Biochemistry and Biophysics, Eds. O.M. Becker, A.D. MacKerell, Jr., B. Roux, and M. Watanabe (Marcel Dekker, New York, 2001), pp. 115-131.

• T.E. Malliavin, F. Dardel (2001) Structure des protéines par RMN. Techniques de l'Ingénieur, AF 6 608.

• B. Hartmann, M.R. Sullivan, L.F. Harris (2001) OR1 & OR2 recognition by the phage 434 cI repressor. University of Minnesota Supercomputing Institute Research Report 120, 1-19.

• A.K. Mazur and D.E. Kamashev (2001) Simulated and experimental bending dynamics in DNA with and without A-tracts. Preprint physics/0108038.

2000

• L. Ayadi, C. Coulombeau, R. Lavery (2000) The impact of abasic sites on DNA flexibility. J. Biomol. Struct. Dyn. 17, 645-653.

• S.A. Kozin, G. Bertho, A.K. Mazur, H. Rabesona, J.-P. Girault, T. Haertle, M. Takahashi, P. Debey, G. H. Hoa (2000) Prion peptide folds into water-stable monomeric beta-sheet: Possible molecular trigger of prion disease. J. Pept. Sci. 6, s141.

• I. Lafontaine, R. Lavery (2000) Direct optimization of nucleic acid sequences. Biophys. J. 79, 680-685.

• A.K. Mazur (2000) Theoretical studies of the possible origin of intrinsic static bends in double helical DNA. J. Am. Chem. Soc. 122, 12778-12785.

• R. Rohs, H. Sklenar, R. Lavery, B. Röder (2000) Methylene blue binding to DNA with an alternative GC base sequence: A modelling study. J. Am. Chem. Soc. 122, 2860-2866.

• A. Slama-Schwok, K. Zakrzewska, G. Léger, Y. Leroux, M. Takahashi, E. Kas, P. Debey (2000) Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence. Biophys. J. 78, 2543-2559.

• R. Lavery (2000) Modélisation de l'ADN: de la mécanique à la reconnaissance. Images de la Recherche en Biologie Structurale, CNRS 136-143.

• R. Lavery (2000) G.N. Ramachandran: perspective on stereochemistry of polypeptide chain conformations. Theoret. Chem. Acc., New Century Issue, 103, 257-258. 

• G. Bertucat, R. Lavery, C. Prévost (2000) A mechanism for RecA-promoted homology recognition and strand exchange between single-stranded DNA and duplex DNA via triple-helical intermediates. Proceedings of the XIth Conversation in Biomolecular Stereodynamics, volume I, Eds. R. Sarma and M. Sarma, Adenine Press, New York, 147-153.

• Y. Timsit (2000) Polymerase fidelity: a new role for A-DNA. Proceedings of the XIth Conversation in Biomolecular Stereodynamics, Eds. R. Sarma and M. Sarma, Adenine Press 169-176.

• A.K. Mazur (2000) A-tract induced DNA bending is a local non-electrostatic effect. Preprint physics/0002010.

• A.K. Mazur (2000) The physical origin of intrinsic bends in double helical DNA. Preprint physics/0004040.

• A.K. Mazur (2000) Molecular dynamics studies of sequence-directed curvature in bending locus of trypanosome kinetoplast DNA. Preprint physics/0004049.

1999

• L. Ayadi, C. Coulombeau, R. Lavery (1999) Abasic sites in duplex DNA: molecular modelling of sequence-dependent effects on conformation. Biophys. J. 77, 3218-3226.

• L. Ayadi, M. Jourdan, C. Coulombeau, J. Garcia, R. Lavery (1999) Experimental and theoretical studies of the conformational perturbations induced by an abasic site. J. Biomol. Struct. Dyn. 17, 245-257.

• P. Barthe, L. Chiche, N. Declerck, M.A. Delsuc, J.F. Lefèvre, T. Malliavin, J. Mispelter, M.H. Stern, J.M. Lhoste, C. Roumestand (1999) Refined solution structure and backbone dynamics of 15N-labeled C12A-p8^MTCP1 studied by NMR relaxation. J. Biomol. NMR 15, 271-288 .

• H-O. Bertrand, A. Pullman, K. Zakrzewska, B. Hartmann, S. Fermandjian (1999) Determination of a set of parameters for the molecular modelling of the phosphorothioate DNA. Theoret. Chem. Accts. 98, 269-273.

• G. Bertucat, R. Lavery, C. Prevost (1999) A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices. Biophys. J. 77, 1562-1576.

• N. Bruant, D. Flatters, R. Lavery, D. Genest (1999) From atomic to mesoscopic descriptions of the internal dynamics of DNA. Biophys. J. 77, 2366-2376.

• R. Gurlie, T. Ha-Duong, K. Zakrzewska (1999) The role of DNA-protein salt bridges in molecular recognition: a model study. Biopolymers 49, 313-327.

• B. Hartmann, H-O Bertrand, S. Fermandjian (1999) Sequence effects on energetic and structural properties of phosphorothioates DNA: a molecular lodelling study. Nucleic Acids Res. 27(16), 3342-3347.

• I. Lafontaine, R. Lavery (1999) Collective variable modelling of nucleic acids. Curr. Opin. Struct. Biol. 76, 170-176.

• R. Lavery, A. Lebrun (1999) Modelling DNA stretching for physics and biology. Genetica 106, 75-84.

• A. Lebrun, R. Lavery (1999) Modeling DNA deformations induced by minor groove binding proteins. Biopolymers 49, 341-353.

• T.E. Malliavin, H. Desvaux, A. Aumelas, A. Chavanieu, M.A. Delsuc (1999) Quantitative measurement of longitudinal and transverse cross-relaxation rates: an application to the analysis of the internal dynamics of ranalexin in water and trifluoroethanol. J. Magn. Reson. 140, 189-199.

• T.E. Malliavin, H. Desvaux, M.A. Delsuc (1999) Quantitative determination of longitudinal and transverse cross-relaxation rates. J. Chim. Phys. 96, 1608-1615.

• A.K. Mazur (1999) Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion. J. Chem. Phys. 111, 1407-1414.

• A.K. Mazur (1999) Internal correlations in minor groove profiles of experimental and computed B-DNA conformations. J. Mol. Biol. 290, 373-377.

• R. Rohs, C. Etchebest, R. Lavery (1999) Unraveling proteins: a molecular mechanics study. Biophys. J. 76, 2760-2768.

• Y. Timsit, M. Shatzky-Schwartz, Z. Shakked (1999) Left-handed DNA crossovers. Implications for DNA-DNA recognition and structural alterations. J. Biomol. Struct. Dyn. 16, 775-786.

• Y. Timsit (1999) DNA structure and polymerase fidelity. J. Mol. Biol. 293, 835-853.

• C. Tisné, B. Hartmann, M. Delepierre (1999) NF-kB binding mechanism: an NMR and modelling study of a GGG → CTC mutation. Biochemistry 38(13), 3883-3894.

• C. Tisné, M. Delepierre, B. Hartmann (1999) How NF-kB can be attracted by its cognate DNA. J. Mol. Biol. 293(1), 139-150.

• E. Stofer, C. Chipot, R. Lavery (1999) Free energy calculations of Watson-Crick base pairing in aqueous solution. J. Am. Chem. Soc. 121, 9503-9508.

• T. Strick, J.F. Allemand, D. Bensimon, R. Lavery, V. Croquette (1999) Phase coexistence in a single DNA molecule. Stat. Phys. 263, 392-404.

• J.F. Allemand, D. Bensimon, V. Croquette, R. Lavery, B. Maier, T. Strick (1999) Molecular Jokari. Biofutur 26-27.

• R. Lavery, K. Zakrzewska (1999) Base and base pair morphologies, helical parameters and definitions. dans Oxford Handbook of Nucleic Acid Structure Eds. S. Neidle, Oxford University Press 36-76.

• T. Strick, J.F. Allemand, D. Bensimon, V. Croquette, C. Bouchiat, M. Mézard, R. Lavery (1999) Twisting a single DNA molecule: experiments and models. dans Topological Concepts in Low Dimensional Systems Eds. Corti EDP Sciences.

•  K. Zakrzewska, R. Lavery (1999) Modelling DNA-protein interactions. dans Computational Molecular Biology Eds. J. Leszynski Vol. 8 441-483.

• G. Bertucat, R. Lavery, C. Prévost (1999) Sequence recognition in the minor groove of a duplex DNA by a homologous single strand complexed to RecA protein: A multi-step recognition process. J. Biomol. Struct. Dyn. 16, 1355.

• R. Lavery (1999) Simulation moléculaire: macromolécules biologiques et systèmes complexes. Actes des 3^ème entretiens de la Physique, Paris.

• C. Prévost, E. Meneses, R. Lavery (1999) Modelling the adsorption of macromolecules in surfaces: The case of actin. CECAM Worskshop: Molecular Modeling of proteins at interfaces, 20-24 septembre 1999.

• AK. Mazur (1999) A minimal model of B-DNA. Preprint physics /9907028.

• R. Lavery (1999) Conformational Chemistry and the Living world: From Sequence to Function. Conference proceedings. Eds. R. Lavery, J. Tomasi, Theoretical Chemistry Accounts, Springer, Würzburg, Allemagne 101.