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Accueil du site > Équipes > Modélisation des Macromolécules Biologiques (L. Monticelli) > Publications

Publications

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2016 [Top] 4
359.  Protein-DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors.   
Etheve L, Martin J, Lavery R
(2016) Nucleic Acids Res 

358.  Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.   
Etheve L, Martin J, Lavery R
(2016) Nucleic Acids Res 44 : 1440-8

357.  Implication of Terminal Residues at Protein-Protein and Protein-DNA Interfaces.   
Martin OM, Etheve L, Launay G, Martin J
(2016) PLoS One 11 : e0162143-e0162143

356.  The C-terminal Domains of Apoptotic BH3-only Proteins Mediate Their Insertion into Distinct Biological Membranes.   
Andreu-Fernandez V, Garcia-Murria MJ, Bano-Polo M, Martin J, Monticelli L, Orzaez M, Mingarro I
(2016) J Biol Chem 291 : 25207-25216

2015 [Top] 7
355.  Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics.   
Pasi M, Maddocks JH, Lavery R
(2015) Nucleic Acids Res 43 : 2412-23

354.  Internal Normal Mode Analysis (iNMA) Applied to Protein Conformational Flexibility.   
Frezza E, Lavery R
(2015) J Chem Theory Comput 11 : 5503-12

353.  MARTINI Coarse-Grained Models of Polyethylene and Polypropylene.   
Panizon E, Bochicchio D, Monticelli L, Rossi G
(2015) J Phys Chem B 119 : 8209-16

352.  The C-terminal ?-helix of YsxC is essential for its binding to 50S ribosome and rRNAs.   
Wicker-Planquart C, Ceres N, Jault JM
(2015) FEBS Lett 589 : 2080-6

351.  Coarse-grained force fields for molecular simulations.   
Barnoud J, Monticelli L
(2015) Methods Mol Biol 1215 : 125-49

350.  C?? fullerene promotes lung monolayer collapse.   
Barnoud J, Urbini L, Monticelli L
(2015) J R Soc Interface 12 : 20140931-20140931

349.  Calculating the free energy of transfer of small solutes into a model lipid membrane: Comparison between metadynamics and umbrella sampling.   
Bochicchio D, Panizon E, Ferrando R, Monticelli L, Rossi G
(2015) J Chem Phys 143 : 144108-144108

2014 [Top] 21
348.  Polystyrene Nanoparticles Perturb Lipid Membranes   
Rossi G, Barnoud J, Monticelli L
(2014) Journal of Physical Chemistry Letters 5 : 241-246

347.  Analyzing ion distributions around DNA.   
Lavery R, Maddocks JH, Pasi M, Zakrzewska K
(2014) Nucleic Acids Res 42 : 8138-49

346.  Plasticity and conformational equilibria of influenza fusion peptides in model lipid bilayers.   
Haria NR, Monticelli L, Fraternali F, Lorenz CD
(2014) Biochim Biophys Acta 1838 : 1169-79

345.  Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA.   
Dans PD, Faustino I, Battistini F, Zakrzewska K, Lavery R, Orozco M
(2014) Nucleic Acids Res 42 : 11304-20

344.  BCL2DB: database of BCL-2 family members and BH3-only proteins.   
Rech De Laval V, Deleage G, Aouacheria A, Combet C
(2014) Database (Oxford) 2014 : bau013-bau013

343.  Evolution of bacterial protein-tyrosine kinases and their relaxed specificity toward substrates.   
Shi L, Ji B, Kolar-Znika L, Boskovic A, Jadeau F, Combet C, Grangeasse C, Franjevic D, Talla E, Mijakovic I
(2014) Genome Biol Evol 6 : 800-17

342.  Ultradeep pyrosequencing and molecular modeling identify key structural features of hepatitis B virus RNase H, a putative target for antiviral intervention.   
Hayer J, Rodriguez C, Germanidis G, Deleage G, Zoulim F, Pawlotsky JM, Combet C
(2014) J Virol 88 : 574-82

341.  Stable polyglutamine dimers can contain ?-hairpins with interdigitated side chains-but not ?-helices, ?-nanotubes, ?-pseudohelices, or steric zippers.   
Miettinen MS, Monticelli L, Nedumpully-Govindan P, Knecht V, Ignatova Z
(2014) Biophys J 106 : 1721-8

340.  The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations.   
Pan J, Cheng X, Monticelli L, Heberle FA, Ku?erka N, Tieleman DP, Katsaras J
(2014) Soft Matter 10 : 3716-25

339.  CLAP: a web-server for automatic classification of proteins with special reference to multi-domain proteins.   
Gnanavel M, Mehrotra P, Rakshambikai R, Martin J, Srinivasan N, Bhaskara RM
(2014) BMC Bioinformatics 15 : 343-343

338.  ?ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.   
Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T, Dans PD, Jayaram B, Lankas F, Laughton C, Mitchell J, Osman R, Orozco M, Perez A, Petkevi?i?t? D, Spackova N, Sponer J, Zakrzewska K, Lavery R
(2014) Nucleic Acids Res 42 : 12272-83

337.  MapZ marks the division sites and positions FtsZ rings in Streptococcus pneumoniae.   
Fleurie A, Lesterlin C, Manuse S, Zhao C, Cluzel C, Lavergne JP, Franz-Wachtel M, Macek B, Combet C, Kuru E, VanNieuwenhze MS, Brun YV, Sherratt D, Grangeasse C
(2014) Nature 516 : 259-62

336.  Interplay of the serine/threonine-kinase StkP and the paralogs DivIVA and GpsB in pneumococcal cell elongation and division.   
Fleurie A, Manuse S, Zhao C, Campo N, Cluzel C, Lavergne JP, Freton C, Combet C, Guiral S, Soufi B, Macek B, Kuru E, VanNieuwenhze MS, Brun YV, Di Guilmi AM, Claverys JP, Galinier A, Grangeasse C
(2014) PLoS Genet 10 : e1004275-e1004275

335.  Polystyrene Nanoparticles Perturb Lipid Membranes.   
Rossi G, Barnoud J, Monticelli L
(2014) J Phys Chem Lett 5 : 241-6

334.  Benchmarking protein-protein interface predictions: why you should care about protein size.   
Martin J
(2014) Proteins 82 : 1444-52

333.  Hydrophobic compounds reshape membrane domains.   
Barnoud J, Rossi G, Marrink SJ, Monticelli L
(2014) PLoS Comput Biol 10 : e1003873-e1003873

332.  Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations.   
Bouvier B
(2014) Phys Chem Chem Phys 16 : 48-60

331.  Modeling the effect of nano-sized polymer particles on the properties of lipid membranes.   
Rossi G, Monticelli L
(2014) J Phys Condens Matter 26 : 503101-503101

330.  Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast.   
Spor A, Kvitek DJ, Nidelet T, Martin J, Legrand J, Dillmann C, Bourgais A, De Vienne D, Sherlock G, Sicard D
(2014) Evolution 68 : 772-90

329.  The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins.   
Bhaskara RM, Mehrotra P, Rakshambikai R, Gnanavel M, Martin J, Srinivasan N
(2014) Mol Biosyst 10 : 1082-93

328.  Lipid membranes as solvents for carbon nanoparticles.   
Barnoud J, Rossi G, Monticelli L
(2014) Phys Rev Lett 112 : 068102-068102

2013 [Top] 10
327.  HBVdb: a knowledge database for Hepatitis B Virus.   
Hayer J, Jadeau F, Deleage G, Kay A, Zoulim F, Combet C
(2013) Nucleic Acids Res 41 : D566-70

326.  Partitioning and solubility of C-60 fullerene in lipid membranes   
Rossi G, Barnoud J, Monticelli L
(2013) Physica scripta 87

325.  Free energy of WALP23 dimer association in DMPC, DPPC, and DOPC bilayers.   
Castillo N, Monticelli L, Barnoud J, Tieleman DP
(2013) Chem Phys Lipids 169 : 95-105

324.  Evolution of Bcl-2 homology motifs: homology versus homoplasy.   
Aouacheria A, Rech De Laval V, Combet C, Hardwick JM
(2013) Trends Cell Biol 23 : 103-11

323.  Anomalous and normal diffusion of proteins and lipids in crowded lipid membranes.   
Javanainen M, Hammaren H, Monticelli L, Jeon JH, Miettinen MS, Martinez-Seara H, Metzler R, Vattulainen I
(2013) Faraday Discuss 161 : 397-417

322.  Temperature dependence of the DNA double helix at the nanoscale: structure, elasticity, and fluctuations.   
Meyer S, Jost D, Theodorakopoulos N, Peyrard M, Lavery R, Everaers R
(2013) Biophys J 105 : 1904-14

321.  BRCA1-Dependent Translational Regulation in Breast Cancer Cells.   
Dacheux E, Vincent A, Nazaret N, Combet C, Wierinckx A, Mazoyer S, Diaz JJ, Lachuer J, Venezia ND
(2013) PLoS One 8 : e67313-e67313

320.  Force fields for classical molecular dynamics.   
Monticelli L, Tieleman DP
(2013) Methods Mol Biol 924 : 197-213

319.  Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations   
Bulacu M, Goga N, Zhao W, Rossi G, Monticelli L, Periole X, Tieleman DP, Marrink SJ
(2013) JOURNAL OF CHEMICAL THEORY AND COMPUTATION  9 : 3282-3292

318.  Interaction of pristine and functionalized carbon nanotubes with lipid membranes.   
Baoukina S, Monticelli L, Tieleman DP
(2013) J Phys Chem B 117 : 12113-23

2012 [Top] 14
317.  Assessing polyglutamine conformation in the nucleating event by molecular dynamics simulations.   
Miettinen MS, Knecht V, Monticelli L, Ignatova Z
(2012) J Phys Chem B 116 : 10259-65

316.  Towards a molecular view of transcriptional control.   
Zakrzewska K, Lavery R
(2012) Curr Opin Struct Biol 22 : 160-7

315.  Interaction of C70 fullerene with the Kv1.2 potassium channel.   
Monticelli L, Barnoud J, Orlowski A, Vattulainen I
(2012) Phys Chem Chem Phys 14 : 12526-33

314.  Mutagenesis of the bovSERPINA3-3 demonstrates the requirement of aspartate-371 for intermolecular interaction and formation of dimers.   
Blanchet X, Pere-Brissaud A, Duprat N, Pinault E, Delourme D, Ouali A, Combet C, Maftah A, Pelissier P, Bremaud L
(2012) Protein Sci 21 : 977-86

313.  Arbitrary protein-protein docking targets biologically relevant interfaces.   
Martin J, Lavery R
(2012) BMC Biophys 5 : 7-7

312.  Mechanism for translocation of fluoroquinolones across lipid membranes.   
Cramariuc O, Rog T, Javanainen M, Monticelli L, Polishchuk AV, Vattulainen I
(2012) Biochim Biophys Acta 1818 : 2563-71

311.  Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA.   
Wilhelm M, Mukherjee A, Bouvier B, Zakrzewska K, Hynes JT, Lavery R
(2012) J Am Chem Soc 134 : 8588-96

310.  BYKdb: the Bacterial protein tYrosine Kinase database.   
Jadeau F, Grangeasse C, Shi L, Mijakovic I, Deleage G, Combet C
(2012) Nucleic Acids Res 40 : D321-4

309.  A coarse-grained MARTINI model of polyethylene glycol and of polyoxyethylene alkyl ether surfactants.   
Rossi G, Fuchs PF, Barnoud J, Monticelli L
(2012) J Phys Chem B 116 : 14353-62

308.  A Protein Solvation Model Based on Residue Burial   
Ceres N, Pasi M, Lavery R
(2012) JOURNAL OF CHEMICAL THEORY AND COMPUTATION  8 : 2141-2144

307.  Mechanism of taq DNA polymerase inhibition by fullerene derivatives: insight from computer simulations.   
Nedumpully Govindan P, Monticelli L, Salonen E
(2012) J Phys Chem B 116 : 10676-83

306.  Exploring polymorphisms in B-DNA helical conformations.   
Dans PD, Perez A, Faustino I, Lavery R, Orozco M
(2012) Nucleic Acids Res 40 : 10668-78

305.  Mutations that alter use of hepatitis C virus cell entry factors mediate escape from neutralizing antibodies.   
Fofana I, Fafi-Kremer S, Carolla P, Fauvelle C, Zahid MN, Turek M, Heydmann L, Cury K, Hayer J, Combet C, Cosset FL, Pietschmann T, Hiet MS, Bartenschlager R, Habersetzer F, Doffoel M, Keck ZY, Foung SK, Zeisel MB, Stoll-Keller F, Baumert TF
(2012) Gastroenterology 143 : 223-233

304.  On atomistic and coarse-grained models for C60 fullerene.   
Monticelli L
(2012) J Chem Theory Comput 8 : 1370-1378

2011 [Top] 6
303.  Protein-DNA recognition triggered by a DNA conformational switch.   
Bouvier B, Zakrzewska K, Lavery R
(2011) Angew Chem Int Ed Engl 50 : 6516-8

302.  Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.   
Regad L, Martin J, Camproux AC
(2011) BMC Bioinformatics 12 : 247-247

301.  CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures.   
Blanchet C, Pasi M, Zakrzewska K, Lavery R
(2011) Nucleic Acids Res 39 : W68-73

300.  Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case   
Rossi G, Monticelli L, Puisto SR, Vattulainen I,Ala-Nissila T
(2011) SOFT MATTER 7 : 698-708

299.  [The directory of French biological resources centres/biobanks].   
Jadeau F, Barthelaix A, Burgun A, Deleval C, Garcelon N, Gele P, Libersa C, Savonnet M, Tabone E, Combet C
(2011) Med Sci (Paris) 27 : 895-7

298.  A MARTINI Coarse-Grained Model of a Thermoset Polyester Coating   
Rossi G, Giannakopoulos I, Monticelli L, Rostedt NKJ, Puisto SR, Lowe C, Taylor AC, Vattulainen I, Ala-Nissila T
(2011) MACROMOLECULES 44 : 6198-6208

2010 [Top] 12
297.  ViralORFeome: an integrated database to generate a versatile collection of viral ORFs.     
Pellet J, Tafforeau L, Lucas-Hourani M, Navratil V, Meyniel L, Achaz G, Guironnet-Paquet A, Aublin-Gex A, Caignard G, Cassonnet P, Chaboud A, Chantier T, Deloire A, Demeret C, Le Breton M, Neveu G, Jacotot L, Vaglio P, Delmotte S, Gautier C, Combet C, Deleage G, Favre M, Tangy F, Jacob Y, Andre P, Lotteau V, Rabourdin-Combe C, Vidalain PO
(2010) Nucleic Acids Res 38 : D371-8

296.  Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data     
Nuel G, Regad L, Martin J, Camproux AC,
(2010) ALGORITHMS FOR MOLECULAR BIOLOGY 5 : 15-15

295.  Classification of protein kinases on the basis of both kinase and non-kinase regions.     
Martin J, Anamika K, Srinivasan N
(2010) PLoS One 5 : e12460-e12460

294.  Optical Properties of Guanine Nanowires: Experimental and Theoretical Study     
Changenet-Barret P, Emanuele E, Gustavsson T, Improta R, Kotlyar AB, Markovitsi D, Vaya I, Zakrzewska K, Zikich D
(2010) JOURNAL OF PHYSICAL CHEMISTRY C 114 : 14339-14346

293.  A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.     
Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, Cheatham T, Dixit S, Jayaram B, Lankas F, Laughton C, Maddocks JH, Michon A, Osman R, Orozco M, Perez A, Singh T, Spackova N, Sponer J
(2010) Nucleic Acids Res 38 : 299-313

292.  Free volume theory applied to lateral diffusion in Langmuir monolayers: atomistic simulations for a protein-free model of lung surfactant.   
Javanainen M, Monticelli L, Bernardino De La Serna J, Vattulainen I.
(2010) LANGMUIR  26 : 15436-44

291.  Membrane proteins diffuse as dynamic complexes with lipids.   
Niemelä PS, Miettinen MS, Monticelli L, Hammaren H, Bjelkmar P, Murtola T, Lindahl E, Vattulainen I
(2010) J Am Chem Soc 132 : 7574-7575

290.  Finite Markov Chain Embedding for the Exact Distribution of Patterns in a Set of Random Sequences     
Martin J, Regad L, Camproux AC, Nuel G
(2010) ADVANCES IN DATA ANALYSIS - THEORY AND APPLICATIONS TO RELIABILITY AND INFERENCE, DATA MINING, BIOINFORMATICS, LIFETIME DATA, AND NEURAL NETWORKS  : 171-180

289.  Mining protein loops using a structural alphabet and statistical exceptionality.     
Regad L, Martin J, Nuel G, Camproux AC
(2010) BMC Bioinformatics 11 : 75-75

288.  Membrane protein dynamics from femtoseconds to seconds   
Kandt C, Monticelli L
(2010) Methods Mol Biol 654 : 423-440

287.  Interpretation of 2H-NMR experiments on the orientation of the transmembrane helix WALP23 by computer simulations.   
Monticelli L, Tieleman DP, Fuchs PF
(2010) BIOPHYSICAL JOURNAL 99 : 1455-64

286.  Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way     
Martin J,
(2010) PLOS COMPUTATIONAL BIOLOGY 6 : e1000821-e1000821

2009 [Top] 14
285.  Effects of carbon nanoparticles on lipid membranes: a molecular simulation perspective   
Monticelli L, Salonen E, Ke, PC, Vattulainen I
(2009) SOFT MATTER 22 : 4433-4445

284.  The euHCVdb suite of in silico tools for investigating the structural impact of mutations in hepatitis C virus proteins.   
Combet C, Bettler E, Terreux R, Garnier N, Deleage G
(2009) Infect Disord Drug Targets 9 : 272-8

283.  Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies.     
Zakrzewska K, Bouvier B, Michon A, Blanchet C, Lavery R
(2009) Phys Chem Chem Phys 11 : 10712-21

282.  Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling.     
Engelen S, Trojan LA, Sacquin-Mora S, Lavery R, Carbone A
(2009) PLoS Comput Biol 5 : e1000267-e1000267

281.  PDB_REDO: automated re-refinement of X-ray structure models in the PDB.     
Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G
(2009) J Appl Crystallogr 42 : 376-384

280.  Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.     
Durrieu MP, Bond PJ, Sansom MS, Lavery R, Baaden M
(2009) Chemphyschem 10 : 1548-52

279.  Local and global effects of strong DNA bending induced during molecular dynamics simulations.     
Curuksu J, Zacharias M, Lavery R, Zakrzewska K
(2009) Nucleic Acids Res 37 : 3766-73

278.  Deforming DNA: from physics to biology.     
Prevost C, Takahashi M, Lavery R
(2009) Chemphyschem 10 : 1399-404

277.  Modeling the Mechanical Response of Proteins to Anisotropic Deformation     
Sacquin-Mora S, Lavery R
(2009) CHEMPHYSCHEM 10 : 115-118

276.  Visualization of complex processes in lipid systems using computer simulations and molecular graphics.   
Telenius J, Vattulainen I, Monticelli L.
(2009) Methods Mol Biol 580 : 317-38

275.  Dynamic properties of a psychrophilic alpha-amylase in comparison with a mesophilic homologue.   
Pasi M, Riccardi L, Fantucci P, De Gioia L, Papaleo E
(2009) J Phys Chem B 113 : 13585-95

274.  Modeling the mechanical response of proteins to anisotropic deformation.   
Sacquin-Mora S, Lavery R
(2009) Chemphyschem 10 : 115-8

273.  A free energy pathway for the interaction of the SRY protein with its binding site on DNA from atomistic simulations.     
Bouvier B, Lavery R
(2009) J Am Chem Soc 131 : 9864-5

272.  Conformational analysis of nucleic acids revisited: Curves+.     
Lavery R, Moakher M, Maddocks JH, Petkeviciute D, Zakrzewska K
(2009) Nucleic Acids Res 37 : 5917-29

2008 [Top] 18
271.  Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature.     
Jadeau F, Bechet E, Cozzone AJ, Deleage G, Grangeasse C, Combet C
(2008) Bioinformatics 24 : 2427-30

270.  Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases.   
Papaleo E, Pasi M, Riccardi L, Sambi I, Fantucci P, De Gioia L
(2008) FEBS Lett 582 : 1008-18

269.  The MARTINI coarse-grained force field: Extension to proteins   
Monticelli L, Kandasamy SK, Periole X, Larson RG, Tieleman DP, Marrink SJ
(2008) JOURNAL OF CHEMICAL THEORY AND COMPUTATION  4 : 819-834

268.  Structural deformation upon protein-protein interaction: a structural alphabet approach.     
Martin J, Regad L, Lecornet H, Camproux AC
(2008) BMC Struct Biol 8 : 12-12

267.  Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites.   
Curuksu J, Zakrzewska K, Zacharias M
(2008) Nucleic Acids Res 36 : 2268-83

266.  Transcriptional slippage prompts recoding in alternate reading frames in the hepatitis C virus (HCV) core sequence from strain HCV-1.     
Ratinier M, Boulant S, Combet C, Targett-Adams P, McLauchlan J, Lavergne JP
(2008) J Gen Virol 89 : 1569-78

265.  The molecular mechanism of lipid monolayer collapse.   
Baoukina S, Monticelli L, Risselada HJ, Marrink SJ, Tieleman DP
(2008) Proc Natl Acad Sci U S A 105 : 10803-8

264.  Atomistic Modeling of the Membrane-Embedded Synaptic Fusion Complex: a Grand Challenge Project on the DEISA HPC Infrastructure     
Krieger E, Leger L, Durrieu MP, Taib N, Bond P, Laguerre M, Lavery R, Sansom MSP, Baaden M
(2008) PARALLEL COMPUTING: ARCHITECTURES, ALGORITHNMS AND APPLICATIONS Book Series: Advances in Parallel Computing 15 : 729-736

263.  Interactions between neuronal fusion proteins explored by molecular dynamics.     
Durrieu MP, Lavery R, Baaden M
(2008) Biophys J 94 : 3436-46

262.  Protein-DNA recognition: Breaking the combinatorial barrier     
Deremble C, Lavery R, Zakrzewska K
(2008) COMPUTER PHYSICS COMMUNICATIONS 179 : 112-119

261.  Comparative kinomics of human and chimpanzee reveal unique kinship and functional diversity generated by new domain combinations     
Anamika K, Martin J, Srinivasan N
(2008) BMC GENOMICS 9 : 625-625

260.  Molecular simulation of multistate peptide dynamics: a comparison between microsecond timescale sampling and multiple shorter trajectories.   
Monticelli L, Sorin EJ, Tieleman DP, Pande VS, Colombo G
(2008) J Comput Chem 29 : 1740-52

259.  Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.     
Martin J, Regad L, Etchebest C, Camproux AC
(2008) Proteins 73 : 672-89

258.  On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes.     
Mukherjee A, Lavery R, Bagchi B, Hynes JT
(2008) J Am Chem Soc 130 : 9747-55

257.  In silico local structure approach: a case study on outer membrane proteins.     
Martin J, De Brevern AG, Camproux AC
(2008) Proteins 71 : 92-109

256.  Computer simulation study of fullerene translocation through lipid membranes.   
Wong-Ekkabut J, Baoukina S, Triampo W, Tang IM, Tieleman DP, Monticelli L
(2008) Nat Nanotechnol 3 : 363-8

255.  Identification of protein interaction partners and protein-protein interaction sites.     
Sacquin-Mora S, Carbone A, Lavery R
(2008) J Mol Biol 382 : 1276-89

254.  Theoretical description of chromosome architecture after multiple back-crossing.     
Rodolphe F, Martin J, Della-Chiesa E
(2008) Theor Popul Biol 73 : 289-99

2007 [Top] 10
253.  Probing the flexibility of the bacterial reaction center: the wild-type protein is more rigid than two site-specific mutants.     
Sacquin-Mora S, Sebban P, Derrien V, Frick B, Lavery R, Alba-Simionesco C
(2007) Biochemistry 46 : 14960-8

252.  Theory and simulation     
Lavery R , Sharp KA
(2007) CURRENT OPINION IN STRUCTURAL BIOLOGY 17 : 147-148

251.  Locating the active sites of enzymes using mechanical properties.     
Sacquin-Mora S, Laforet E, Lavery R
(2007) Proteins 67 : 350-9

250.  An elevated level of cholesterol impairs self-assembly of pulmonary surfactant into a functional film.   
Leonenko Z, Gill S, Baoukina S, Monticelli L, Doehner J, Gunasekara L, Felderer F, Rodenstein M, Eng LM, Amrein M
(2007) Biophys J 93 : 674-83

249.  euHCVdb: the European hepatitis C virus database.     
Combet C, Garnier N, Charavay C, Grando D, Crisan D, Lopez J, Dehne-Garcia A, Geourjon C, Bettler E, Hulo C, Le Mercier P, Bartenschlager R, Diepolder H, Moradpour D, Pawlotsky JM, Rice CM, Trepo C, Penin F, Deleage G
(2007) Nucleic Acids Res 35 : D363-6

248.  Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations.   
Baoukina S, Monticelli L, Marrink SJ, Tieleman DP
(2007) Langmuir 23 : 12617-23

247.  Protein mechanics: a route from structure to function.     
Lavery R, Sacquin-Mora S
(2007) J Biosci 32 : 891-8

246.  A molecular dynamics study of slow base flipping in DNA using conformational flooding.     
Bouvier B, Grubmuller H
(2007) Biophys J 93 : 770-86

245.  Effect of lipid peroxidation on the properties of lipid bilayers: a molecular dynamics study.   
Wong-Ekkabut J, Xu Z, Triampo W, Tang IM, Tieleman DP, Monticelli L
(2007) Biophys J 93 : 4225-36

244.  The molecular mechanism of monolayer-bilayer transformations of lung surfactant from molecular dynamics simulations.   
Baoukina S, Monticelli L, Amrein M, Tieleman DP
(2007) Biophys J 93 : 3775-82

2006 [Top] 15
243.  Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins.   
Tieleman DP, Maccallum JL, Ash WL, Kandt C, Xu Z, Monticelli L
(2006) J Phys Condens Matter 18 : S1221-34

242.  Structural investigation of syringomycin-E using molecular dynamics simulation and NMR.   
Matyus E, Monticelli L, Kover KE, Xu Z, Blasko K, Fidy J, Tieleman DP
(2006) Eur Biophys J 35 : 459-67

241.  Analysis of an optimal hidden Markov model for secondary structure prediction.     
Martin J, Gibrat JF, Rodolphe F
(2006) BMC Struct Biol 6 : 25-25

240.  Assessing the Influence of Electrostatic Schemes on Molecular Dynamics Simulations of Secondary Structure Forming Peptides   
Monticelli L, Simoes C, Belvisi L, Colombo G
(2006) J Phys Condens Matter 18 : S329-S345

239.  DNA-directed assembly of polyanilines: modified cytosine nucleotides transfer sequence programmability to a conjoined polymer.     
Datta B, Schuster GB, McCook A, Harvey SC, Zakrzewska K
(2006) J Am Chem Soc 128 : 14428-9

238.  Kinking occurs during molecular dynamics simulations of small DNA minicircles.     
Lankas F, Lavery R, Maddocks JH
(2006) Structure 14 : 1527-34

237.  Identification of non random motifs in loops using a structural alphabet     
Regad L , Martin J , Camproux AC
(2006) Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology  : 92-100

236.  A comprehensive system for consistent numbering of HCV sequences, proteins and epitopes.     
Kuiken C, Combet C, Bukh J, Shin-I T, Deleage G, Mizokami M, Richardson R, Sablon E, Yusim K, Pawlotsky JM, Simmonds P,
(2006) Hepatology 44 : 1355-61

235.  Web services interface to run protein sequence tools on grid, testcase of protein sequence alignment     
Blanchet C , Combet C , Daric V , Deleage G
(2006) Biological and Medical Data Analysis 4345 : 240-249

234.  Investigating the local flexibility of functional residues in hemoproteins.     
Sacquin-Mora S, Lavery R
(2006) Biophys J 90 : 2706-17

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

232.  Dynamics and stability of E-cadherin dimers.   
Cailliez F, Lavery R
(2006) Biophys J 91 : 3964-71

231.  Wringing out DNA.     
Lionnet T, Joubaud S, Lavery R, Bensimon D, Croquette V
(2006) Phys Rev Lett 96 : 178102-178102

230.  GPS@ bioinformatics portal: from network to EGEE grid.   
Blanchet C, Lefort V, Combet C, Deleage G
(2006) Stud Health Technol Inform 120 : 187-93

229.  Hepatitis C databases, principles and utility to researchers.     
Kuiken C, Mizokami M, Deleage G, Yusim K, Penin F, Shin-I T, Charavay C, Tao N, Crisan D, Grando D, Dalwani A, Geourjon C, Agrawal A, Combet C
(2006) Hepatology 43 : 1157-65

2005 [Top] 14
228.  Recognizing DNA.     
Lavery R
(2005) Q Rev Biophys 38 : 339-44

227.  Choosing the optimal hidden Markov model for secondary-structure prediction     
Martin J, Gibrat JF, Rodolphe F
(2005) IEEE INTELLIGENT SYSTEMS 20 : 19-25

226.  Exciton states of dynamic DNA double helices: alternating dCdG sequences.     
Emanuele E, Zakrzewska K, Markovitsi D, Lavery R, Millie P
(2005) J Phys Chem B 109 : 16109-18

225.  UV spectra and excitation delocalization in DNA: influence of the spectral width.     
Emanuele E, Markovitsi D, Millie P, Zakrzewska K
(2005) Chemphyschem 6 : 1387-92

224.  Macromolecular recognition.     
Deremble C, Lavery R
(2005) Curr Opin Struct Biol 15 : 171-5

223.  Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes.     
Simmonds P, Bukh J, Combet C, Deleage G, Enomoto N, Feinstone S, Halfon P, Inchauspe G, Kuiken C, Maertens G, Mizokami M, Murphy DG, Okamoto H, Pawlotsky JM, Penin F, Sablon E, Shin-I T, Stuyver LJ, Thiel HJ, Viazov S, Weiner AJ, Widell A
(2005) Hepatology 42 : 962-73

222.  Mechanism of helix nucleation and propagation: microscopic view from microsecond time scale MD simulations.   
Monticelli L, Tieleman DP, Colombo G
(2005) J Phys Chem B 109 : 20064-7

221.  Folding and mis-folding of peptides and proteins: insights from molecular simulations.   
De Mori GM, Meli M, Monticelli L, Colombo G
(2005) Mini Rev Med Chem 5 : 353-9

220.  Kinetics study of Bungarus fasciatus venom acetylcholinesterase immobilised on a Langmuir-Blodgett proteo-glycolipidic bilayer.     
Godoy S, Violot S, Boullanger P, Bouchu MN, Leca-Bouvier BD, Blum LJ, Girard-Egrot AP
(2005) Chembiochem 6 : 395-404

219.  Non-additivity in protein-DNA binding.     
O'Flanagan RA, Paillard G, Lavery R, Sengupta AM
(2005) Bioinformatics 21 : 2254-63

218.  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.     
Dixit SB, Beveridge DL, Case DA, Cheatham TE, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Sklenar H, Thayer KM, Varnai P
(2005) Biophys J 89 : 3721-40

217.  Cadherin mechanics and complexation: the importance of calcium binding.     
Cailliez F, Lavery R
(2005) Biophys J 89 : 3895-903

216.  The SuMo server: 3D search for protein functional sites.     
Jambon M, Andrieu O, Combet C, Deleage G, Delfaud F, Geourjon C
(2005) Bioinformatics 21 : 3929-30

215.  Protein secondary structure assignment revisited: a detailed analysis of different assignment methods.     
Martin J, Letellier G, Marin A, Taly JF, De Brevern AG, Gibrat JF
(2005) BMC Struct Biol 5 : 17-17

2004 [Top] 16
214.  DNA and its counterions: a molecular dynamics study.     
Varnai P, Zakrzewska K
(2004) Nucleic Acids Res 32 : 4269-80

213.  Analyzing protein-DNA recognition mechanisms.     
Paillard G, Lavery R
(2004) Structure 12 : 113-22

212.  Investigation of the photoionization mechanism of small aromatic homoclusters     
Bouvier B, Millie P, Mons M
(2004) JOURNAL OF PHYSICAL CHEMISTRY A 108 : 4254-4260

211.  Comparison of the cleavage profiles of oligonucleotide duplexes with or without phosphorothioate linkages by using a chemical nuclease probe.     
Chworos A, Arnaud P, Zakrzewska K, Guga P, Pratviel G, Stec W, Meunier B
(2004) J Biol Inorg Chem 9 : 374-84

210.  Myosin flexibility: structural domains and collective vibrations.     
Navizet I, Lavery R, Jernigan RL
(2004) Proteins 54 : 384-93

209.  The influence of simulation conditions in molecular dynamics investigations of model beta-sheet peptides   
Monticelli L, Colombo G
(2004) THEORETICAL CHEMISTRY ACCOUNTS  112 : 145-157

208.  Computer simulation of the KvAP voltage-gated potassium channel: steered molecular dynamics of the voltage sensor.   
Monticelli L, Robertson KM, MacCallum JL, Tieleman DP
(2004) FEBS Lett 564 : 325-32

207.  Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl.   
Mukhopadhyay P, Monticelli L, Tieleman DP
(2004) Biophys J 86 : 1601-9

206.  Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.     
Beveridge DL, Barreiro G, Byun KS, Case DA, Cheatham TE, Dixit SB, Giudice E, Lankas F, Lavery R, Maddocks JH, Osman R, Seibert E, Sklenar H, Stoll G, Thayer KM, Varnai P, Young MA
(2004) Biophys J 87 : 3799-813

205.  Probing protein mechanics: residue-level properties and their use in defining domains.     
Navizet I, Cailliez F, Lavery R
(2004) Biophys J 87 : 1426-35

204.  Computer Simulations of voltage-gated potassium channel KvAP   
Tieleman DP, Robertson KM, Maccallum JL, Monticelli L
(2004) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  100 : 1071-1078

203.  Sequence and pH effects of LNA-containing triple helix-forming oligonucleotides: physical chemistry, biochemistry, and modeling studies.     
Sun BW, Babu BR, Srensen MD, Zakrzewska K, Wengel J, Sun JS
(2004) Biochemistry 43 : 4160-9

202.  Looking into DNA recognition: zinc finger binding specificity.     
Paillard G, Deremble C, Lavery R
(2004) Nucleic Acids Res 32 : 6673-82

201.  Grid as a bioinformatic tool      
Jacq N, Blanchet C, Combet C, Cornillot E, Duret L, Kurata K, Nakamura H, Silvestre T, Breton V
(2004) PARALLEL COMPUTING  30 : 1093-1107

200.  HCVDB: hepatitis C virus sequences database.   
Combet C, Penin F, Geourjon C, Deleage G
(2004) Appl Bioinformatics 3 : 237-40

199.  Theoretical investigation of small alkali cation-molecule: A model potential approach     
Cezard C, Bouvier B, Brenner V, Defranceschi M, Millie P, Soudan JM, Dognon JP
(2004) JOURNAL OF PHYSICAL CHEMISTRY B 108 : 1497-1506

2003 [Top] 10
198.  Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.     
Giudice E, Lavery R
(2003) J Am Chem Soc 125 : 4998-9

197.  Conformational studies of a bombolitin III-derived peptide mimicking the four-helix bundle structural motif of proteins.   
Schievano E, Mammi S, Monticelli L, Ciardella M, Peggion E
(2003) J Am Chem Soc 125 : 15314-23

196.  Integrated databanks access and sequence/structure analysis services at the PBIL.     
Perriere G, Combet C, Penel S, Blanchet C, Thioulouse J, Geourjon C, Grassot J, Charavay C, Gouy M, Duret L, Deleage G
(2003) Nucleic Acids Res 31 : 3393-9

195.  Comparative study of activities between verbascoside and rutin by docking method      
Gao K, Fan BT, El Fassia N, Zakrzewska K, Jia ZJ, Zheng RL, Panaye A, Couesnon T, Doucet JP
(2003) QSAR  : 18-28

194.  Docking macromolecules with flexible segments.     
Bastard K, Thureau A, Lavery R, Prevost C
(2003) J Comput Chem 24 : 1910-20

193.  Influence of conformational dynamics on the exciton states of DNA oligomers      
Bouvier B, Dognon JP, Lavery R, Markovitsi D, Millie P, Onidas D, Zakrzewska K
(2003) JOURNAL OF PHYSICAL CHEMISTRY B  107 : 13512-13522

192.  Theoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNA.     
Arnaud P, Zakrzewska K, Meunier B
(2003) J Comput Chem 24 : 797-805

191.  Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.     
Giudice E, Varnai P, Lavery R
(2003) Nucleic Acids Res 31 : 1434-43

190.  DNA deformation energetics and protein binding.     
Zakrzewska K
(2003) Biopolymers 70 : 414-23

189.  Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking.     
Harvey SC, Wang C, Teletchea S, Lavery R
(2003) J Comput Chem 24 : 1-9

2002 [Top] 14
188.  A model potential approach to charge resonance phenomena in aromatic cluster ions     
Bouvier B, Brenner V, Millie P, Soudan JM
(2002) JOURNAL OF PHYSICAL CHEMISTRY A 106 : 10326-10341

187.  Selective ligand-induced stabilization of active and desensitized parathyroid hormone type 1 receptor conformations.   
Bisello A, Chorev M, Rosenblatt M, Monticelli L, Mierke DF, Ferrari SL
(2002) J Biol Chem 277 : 38524-30

186.  Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.     
Varnai P, Lavery R
(2002) J Am Chem Soc 124 : 7272-3

185.  Interaction of bombolitin II with a membrane-mimetic environment: an NMR and molecular dynamics simulation approach.   
Monticelli L, Pedini D, Schievano E, Mammi S, Peggion E
(2002) Biophys Chem 101-102 : 577-91

184.  Theoretical study of fast repair of DNA damage by cistanoside C and analogs: mechanism and docking.     
Sperandio O, Fan BT, Zakrzewska K, Jia ZJ, Zheng RL, Panaye A, Doucet JP, El Fassi N
(2002) SAR QSAR Environ Res 13 : 243-60

183.  Structure and mechanics of single biomolecules: experiment and simulation      
Lavery R, Lebrun A, Allemand JF, Bensimon D, Croquette V
(2002) JOURNAL OF PHYSICS-CONDENSED MATTER  14 : R383-R414

182.  Geno3D: automatic comparative molecular modelling of protein.     
Combet C, Jambon M, Deleage G, Geourjon C
(2002) Bioinformatics 18 : 213-4

181.  Dipolar coupling between electronic transitions of the DNA bases and its relevance to exciton states in double helices     
Bouvier B, Gustavsson T, Markovitsi D, Millie P
(2002) CHEMICAL PHYSICS 275 : 75-92

180.  Docking study of cistanoside C to telomeric DNA fragment.     
Delalande O, Gao K, Fan BT, Zakrzewska K, El Fassia N, Jia ZJ, Zheng RL, Panaye A, Doucet JP
(2002) SAR QSAR Environ Res 13 : 675-88

179.  Molecular characterization of a ligand-tethered parathyroid hormone receptor.   
Monticelli L, Mammi S, Mierke DF
(2002) Biophys Chem 95 : 165-72

178.  Heterogeneous nuclear ribonucleoprotein A1 interferes with the binding of the human T cell leukemia virus type 1 rex regulatory protein to its response element.     
Dodon MD, Hamaia S, Martin J, Gazzolo L
(2002) J Biol Chem 277 : 18744-52

177.  Alpha/gamma transitions in the B-DNA backbone.     
Varnai P, Djuranovic D, Lavery R, Hartmann B
(2002) Nucleic Acids Res 30 : 5398-406

176.  HCVDB: Database of hepatitis-C virus sequences and analytical bioinformation tools      
Combet C, Penin F, Geourjon C, Deleage G
(2002) M S-MEDECINE SCIENCES  18 : 639-639

175.  Simulations of nucleic acids and their complexes.     
Giudice E, Lavery R
(2002) Acc Chem Res 35 : 350-7

2001 [Top] 10
174.  Prediction of DNA far-IR absorption spectra based on normal mode analysis      
Bykhovskaia M, Gelmont B, Globus T, Woolard DL, Samuels AC, Duong TH, Zakrzewska K
(2001) THEORETICAL CHEMISTRY ACCOUNTS  106 : 22-27

173.  A simulation of naphthalene matrix isolation: comparison with experiments     
Crepin C, De Pujo P, Bouvier B, Brenner V, Millie P
(2001) CHEMICAL PHYSICS 272 : 243-258

172.  Protein-induced DNA bending: the role of phosphate neutralisation      
Gurlie R, Zakrzewska K
(2001) THEORETICAL CHEMISTRY ACCOUNTS  106 : 83-90

171.  Energetic and conformational aspects of A : T base-pair opening within the DNA double helix      
Giudice E, Varnai P, Lavery R
(2001) CHEMPHYSCHEM  2 : 673-

170.  ANTHEPROT: an integrated protein sequence analysis software with client/server capabilities.     
Deleage G, Combet C, Blanchet C, Geourjon C
(2001) Comput Biol Med 31 : 259-67

169.  Symposium proceedings: Computational Biophys 2000 - Preface      
Lavery R, Richards G
(2001) THEORETICAL CHEMISTRY ACCOUNTS  106 : 1-1

168.  Identification of related proteins with weak sequence identity using secondary structure information.     
Geourjon C, Combet C, Blanchet C, Deleage G
(2001) Protein Sci 10 : 788-97

167.  Conservation of the conformation and positive charges of hepatitis C virus E2 envelope glycoprotein hypervariable region 1 points to a role in cell attachment.     
Penin F, Combet C, Germanidis G, Frainais PO, Deleage G, Pawlotsky JM
(2001) J Virol 75 : 5703-10

166.  Modeling multi-component protein-DNA complexes: the role of bending and dimerization in the complex of p53 dimers with DNA.     
Lebrun A, Lavery R, Weinstein H
(2001) Protein Eng 14 : 233-43

165.  High-speed molecular mechanics searches for optimal DNA interaction sites.     
Lafontaine I, Lavery R
(2001) Comb Chem High Throughput Screen 4 : 707-17

2000 [Top] 9
164.  ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences.     
Lafontaine I, Lavery R
(2000) Biopolymers 56 : 292-310

163.  MPSA: integrated system for multiple protein sequence analysis with client/server capabilities.     
Blanchet C, Combet C, Geourjon C, Deleage G
(2000) Bioinformatics 16 : 286-7

162.  A mechanism for RecA-promoted sequence homology recognition and strand exchange between single-stranded DNA and duplex DNA, via triple-helical intermediates      
Bertucat G, Lavery R, Prevost C
(2000)  DYNAMICS  Sp. Iss. S1 : 147-153

161.  Perspective on "Stereochemistry of polypeptide chain conformations" - Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) J Mol Biol 7 : 95-9      
Lavery R
(2000) THEORETICAL CHEMISTRY ACCOUNTS  103 : 257-258

160.  Methylene blue binding to DNA with alternating GC base sequence: A modeling study      
Rohs R, Sklenar H, Lavery R, Roder B
(2000) JOURNAL OF THE AMERICAN CHEMICAL SOCIETY  122 : 2860-2866

159.  Optimization of nucleic acid sequences.     
Lafontaine I, Lavery R
(2000) Biophys J 79 : 680-5

158.  The impact of abasic sites on DNA flexibility.     
Ayadi L, Coulombeau C, Lavery R
(2000) J Biomol Struct Dyn 17 : 645-53

157.  NPS@: network protein sequence analysis.     
Combet C, Blanchet C, Geourjon C, Deleage G
(2000) Trends Biochem Sci 25 : 147-50

156.  Structural changes induced by binding of the high-mobility group I protein to a mouse satellite DNA sequence.     
Slama-Schwok A, Zakrzewska K, Leger G, Leroux Y, Takahashi M, Kas E, Debey P
(2000) Biophys J 78 : 2543-59

1999 [Top] 15
155.  A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices.     
Bertucat G, Lavery R, Prevost C
(1999) Biophys J 77 : 1562-76

154.  The role of DNA-protein salt bridges in molecular recognition: a model study.     
Gurlie R, Duong TH, Zakrzewska K
(1999) Biopolymers 49 : 313-27

153.  Collective variable modelling of nucleic acids.     
Lafontaine I, Lavery R
(1999) Curr Opin Struct Biol 9 : 170-6

152.  Computational chemistry and the living world: from sequence to function      
Lavery R, Tomasi J
(1999) THEORETICAL CHEMISTRY ACCOUNTS  101 : 1-1

151.  Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation.     
Ayadi L, Coulombeau C, Lavery R
(1999) Biophys J 77 : 3218-26

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

149.  Free energy calculations of Watson-Crick base pairing in aqueous solution      
Stofer E, Chipot C, Lavery R
(1999) JOURNAL OF THE AMERICAN CHEMICAL SOCIETY  121 : 9503-9508

148.  Determination of solution conformations of PrP106-126, a neurotoxic fragment of prion protein, by 1H NMR and restrained molecular dynamics.   
Ragg E, Tagliavini F, Malesani P, Monticelli L, Bugiani O, Forloni G, Salmona M
(1999) Eur J Biochem 266 : 1192-201

147.  From atomic to mesoscopic descriptions of the internal dynamics of DNA.     
Bruant N, Flatters D, Lavery R, Genest D
(1999) Biophys J 77 : 2366-76

146.  Experimental and theoretical studies of the conformational perturbations induced by an abasic site.     
Ayadi L, Jourdan M, Coulombeau C, Garcia J, Lavery R
(1999) J Biomol Struct Dyn 17 : 245-57

145.  Phase coexistence in a single DNA molecule      
Strick T, Allemand JF, Bensimon D, Lavery R, Croquette V
(1999) PHYSICA A  263 : 392-404

144.  Determination of a set of parameters for the molecular modelling of phosphorothioate DNA      
Bertrand HO, Pullman A, Zakrzewska K, Hartmann B, Fermandjian S
(1999) THEORETICAL CHEMISTRY ACCOUNTS  101 : 269-273

143.  Unraveling proteins: a molecular mechanics study.     
Rohs R, Etchebest C, Lavery R
(1999) Biophys J 76 : 2760-8

142.  Molecular jokari      
Allemand JF, Bensimon D, Croquette V, Lavery R, Maier B, Strick T
(1999) BIOFUTUR   : 26-27

141.  Modeling DNA deformations induced by minor groove binding proteins.     
Lebrun A, Lavery R
(1999) Biopolymers 49 : 341-53

1998 [Top] 8
140.  Modeling the mechanics of a DNA oligomer.     
Lebrun A, Lavery R
(1998) J Biomol Struct Dyn 16 : 593-604

139.  DNA curvature and phosphate neutralization: an important aspect of specific protein binding.     
Gurlie R, Zakrzewska K
(1998) J Biomol Struct Dyn 16 : 605-18

138.  Sequence specificity of bacteriophage 434 repressor-operator complexation.     
Duong TH, Zakrzewska K
(1998) J Mol Biol 280 : 31-9

137.  Covalent binding of a bridged pyridinium aldehyde with the self-complementary decamer [d(ATGACGTCAT)](2). Gel analysis, MALDI mass spectrometry and NMR studies      
Cordier C, Convert O, Blais JC, Couesnon T, Zakrzewska K, Mauffret O, Fermandjian S, Dodin G
(1998) JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2 : 115-121

136.  Thoughts on physical chemistry      
Markovitsi D, Lavery R
(1998) ACTUALITE CHIMIQUE   : 26-27

135.  Sequence-dependent dynamics of TATA-Box binding sites.     
Flatters D, Lavery R
(1998) Biophys J 75 : 372-81

134.  A model for parallel triple helix formation by RecA: single-single association with a homologous duplex via the minor groove.     
Bertucat G, Lavery R, Prevost C
(1998) J Biomol Struct Dyn 16 : 535-46

133.  Stretched and overwound DNA forms a Pauling-like structure with exposed bases.     
Allemand JF, Bensimon D, Lavery R, Croquette V
(1998) Proc Natl Acad Sci U S A 95 : 14152-7

1997 [Top] 9
132.  Local DNA stretching mimics the distortion caused by the TATA box-binding protein.     
Lebrun A, Shakked Z, Lavery R
(1997) Proc Natl Acad Sci U S A 94 : 2993-8

131.  Internal coordinate modeling of DNA: Force field comparisons      
Flatters D, Zakrzewska K, Lavery R
(1997) JOURNAL OF COMPUTATIONAL CHEMISTRY  18 : 1043-1055

130.  Influence of drug binding on DNA flexibility: a normal mode analysis.     
Ha Duong T, Zakrzewska K
(1997) J Biomol Struct Dyn 14 : 691-701

129.  Collective-variable Monte Carlo simulation of DNA      
Gabb HA, Prevost C, Bertucat G, Robert CH, Lavery R
(1997) JOURNAL OF COMPUTATIONAL CHEMISTRY  18 : 2001-2011

128.  Distortions of the DNA double helix induced by 1,3-trans-diamminedichloroplatinum(II)-intrastrand cross-link: an internal coordinate molecular modeling study.     
Prevost C, Boudvillain M, Beudaert P, Leng M, Lavery R, Vovelle F
(1997) J Biomol Struct Dyn 14 : 703-14

127.  Calculation and analysis of low frequency normal modes for DNA      
Duong TH, Zakrzewska K
(1997) JOURNAL OF COMPUTATIONAL CHEMISTRY  18 : 796-811

126.  Unusual DNA conformations.     
Lebrun A, Lavery R
(1997) Curr Opin Struct Biol 7 : 348-54

125.  Modelling base pair opening: the role of helical twist      
Bernet J, Zakrzewska K, Lavery R
(1997) THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE  398 : 473-482

124.  Conformational properties of the TATA-box binding sequence of DNA.     
Flatters D, Young M, Beveridge DL, Lavery R
(1997) J Biomol Struct Dyn 14 : 757-65

1996 [Top] 5
123.  DNA: an extensible molecule.     
Cluzel P, Lebrun A, Heller C, Lavery R, Viovy JL, Chatenay D, Caron F
(1996) Science 271 : 792-4

122.  Poisson-Boltzmann calculations for nucleic acids and nucleic acids complexes      
Zakrzewska K, Madami A, Lavery R
(1996) CHEMICAL PHYSICS  204 : 263-269

121.  Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature.     
Sanghani SR, Zakrzewska K, Harvey SC, Lavery R
(1996) Nucleic Acids Res 24 : 1632-7

120.  Modelling extreme stretching of DNA.     
Lebrun A, Lavery R
(1996) Nucleic Acids Res 24 : 2260-7

119.  DNA structural forms.     
Hartmann B, Lavery R
(1996) Q Rev Biophys 29 : 309-68

1995 [Top] 4
118.  JUMNA (JUNCTION MINIMIZATION OF NUCLEIC-ACIDS)      
LAVERY R, ZAKRZEWSKA K, SKLENAR H
(1995) COMPUTER PHYSICS COMMUNICATIONS  91 : 135-158

117.  EFFICIENT CONFORMATIONAL SPACE SAMPLING FOR NUCLEOSIDES USING INTERNAL COORDINATE MONTE-CARLO SIMULATIONS AND A MODIFIED FURANOSE DESCRIPTION      
GABB HA, LAVERY R, PREVOST C
(1995) JOURNAL OF COMPUTATIONAL CHEMISTRY  16 : 667-680

116.  Low-frequency vibrations in alpha-helices: helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories.     
Furois-Corbin S, Smith JC, Lavery R
(1995) Biopolymers 35 : 555-71

115.  Modeling a strand exchange tetraplex conformation.     
Lebrun A, Lavery R
(1995) J Biomol Struct Dyn 13 : 459-64

1994 [Top] 5
114.  Theoretical studies of DNA-RNA hybrid conformations.     
Sanghani SR, Lavery R
(1994) Nucleic Acids Res 22 : 1444-9

113.  Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study.     
Tuffery P, Etchebest C, Popot JL, Lavery R
(1994) J Mol Biol 236 : 1105-22

112.  Modelling DNA conformational mechanics.     
Lavery R, Hartmann B
(1994) Biophys Chem 50 : 33-45

111.  Measuring the geometry of DNA grooves.     
Stofer E, Lavery R
(1994) Biopolymers 34 : 337-46

110.  Fractal properties of a one-dimensional film surface.   
Maksymowicz AZ, Rafa J, Zakrzewska K
(1994) Phys Rev B Condens Matter 50 : 8901-8902

1993 [Top] 10
109.  BI-BII transitions in B-DNA.     
Hartmann B, Piazzola D, Lavery R
(1993) Nucleic Acids Res 21 : 561-8

108.  A possible family of B-like triple helix structures: comparison with the Arnott A-like triple helix.     
Ouali M, Letellier R, Adnet F, Liquier J, Sun JS, Lavery R, Taillandier E
(1993) Biochemistry 32 : 2098-103

107.  Conformations of DNA duplexes containing 8-oxoguanine.     
Poltev VI, Smirnov SL, Issarafutdinova OV, Lavery R
(1993) J Biomol Struct Dyn 11 : 293-301

106.  Packing and recognition of protein structural elements: a new approach applied to the 4-helix bundle of myohemerythrin.     
Tuffery P, Lavery R
(1993) Proteins 15 : 413-25

105.  Looking into the grooves of DNA.     
Boutonnet N, Hui X, Zakrzewska K
(1993) Biopolymers 33 : 479-90

104.  FORCE-FIELD FOR PLATINUM BINDING TO ADENINE      
KOZELKA J, SAVINELLI R, BERTHIER G, FLAMENT JP, LAVERY R
(1993) JOURNAL OF COMPUTATIONAL CHEMISTRY  14 : 45-53

103.  SYMMETRY REDUCTION IN HOMOPOLYMERIC DNA - IMPLICATIONS FOR DNA FINE-STRUCTURE      
ZAKRZEWSKA K, POLTEV VI, OGUEY C, LAVERY R
(1993) THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE  105 : 219-229

102.  Persistence analysis of the static and dynamical helix deformations of DNA oligonucleotides: application to the crystal structure and molecular dynamics simulation of d(CGCGAATTCGCG)2.     
Prevost C, Louise-May S, Ravishanker G, Lavery R, Beveridge DL
(1993) Biopolymers 33 : 335-50

101.  An analysis of the conformational paths of citrate synthase.     
Ech-Cherif El-Kettani MA, Zakrzewska K, Durup J, Lavery R
(1993) Proteins 16 : 393-407

100.  A CRITICAL COMPARISON OF SEARCH ALGORITHMS APPLIED TO THE OPTIMIZATION OF PROTEIN SIDE-CHAIN CONFORMATIONS      
TUFFERY P, ETCHEBEST C, HAZOUT S, LAVERY R
(1993) JOURNAL OF COMPUTATIONAL CHEMISTRY  14 : 790-798

1992 [Top] 7
99.  Conformational sub-states in B-DNA.     
Poncin M, Hartmann B, Lavery R
(1992) J Mol Biol 226 : 775-94

98.  DNA flexibility as a function of allomorphic conformation and of base sequence.     
Poncin M, Piazzola D, Lavery R
(1992) Biopolymers 32 : 1077-103

97.  The fine structure of two DNA dodecamers containing the cAMP responsive element sequence and its inverse. Nuclear magnetic resonance and molecular simulation studies.     
Mauffret O, Hartmann B, Convert O, Lavery R, Fermandjian S
(1992) J Mol Biol 227 : 852-75

96.  A computational and experimental study of the bending induced at a double-triple helix junction.     
Chomilier J, Sun JS, Collier DA, Garestier T, Helene C, Lavery R
(1992) Biophys Chem 45 : 143-52

95.  A comprehensive classification of nucleic acid structural families based on strand direction and base pairing.     
Lavery R, Zakrzewska K, Sun JS, Harvey SC
(1992) Nucleic Acids Res 20 : 5011-6

94.  Strand orientation of [alpha]-oligodeoxynucleotides in triple helix structures: dependence on nucleotide sequence.   
Sun JS, Lavery R
(1992) J Mol Recognit 5 : 93-8

93.  Static and dynamic conformational properties of AT sequences in B-DNA.     
Zakrzewska K
(1992) J Biomol Struct Dyn 9 : 681-93

1991 [Top] 6
92.  Triple helix structures: sequence dependence, flexibility and mismatch effects.     
Sun JS, Mergny JL, Lavery R, Montenay-Garestier T, Helene C
(1991) J Biomol Struct Dyn 9 : 411-24

91.  EVIDENCE FOR THE STOCHASTIC NATURE OF BASE PAIR OPENING IN DNA - A BROWNIAN DYNAMICS SIMULATION      
BRIKI F, RAMSTEIN J, LAVERY R, GENEST D
(1991) JOURNAL OF THE AMERICAN CHEMICAL SOCIETY  113 : 2490-2493

90.  A prospective evaluation of glucose reagent teststrips in the prehospital setting.   
Lavery RF, Allegra JR, Cody RP, Zacharias D, Schreck DM
(1991) Am J Emerg Med 9 : 304-8

89.  MODELING THE B-DNA BASE PAIR OPENING REACTION      
BRIKI F, LAVERY R, GENEST D, RAMSTEIN J
(1991) JOURNAL DE CHIMIE PHYSIQUE ET DE PHYSICO-CHIMIE BIOLOGIQUE  88 : 2567-2572

88.  Theoretical study of ethidium intercalation in triple-stranded DNA and at triplex-duplex junctions.     
Sun JS, Lavery R, Chomilier J, Zakrzewska K, Montenay-Garestier T, Helene C
(1991) J Biomol Struct Dyn 9 : 425-436

87.  A new approach to the rapid determination of protein side chain conformations.     
Tuffery P, Etchebest C, Hazout S, Lavery R
(1991) J Biomol Struct Dyn 8 : 1267-89

1990 [Top] 2
86.  Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI.     
Swaminathan S, Ravishanker G, Beveridge DL, Lavery R, Etchebest C, Sklenar H
(1990) Proteins 8 : 179-93

85.  Base pair opening pathways in B-DNA.     
Ramstein J, Lavery R
(1990) J Biomol Struct Dyn 7 : 915-33

1989 [Top] 7
84.  Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis.     
Sklenar H, Etchebest C, Lavery R
(1989) Proteins 6 : 46-60

83.  The conformation and stability of ribonucleic acids: modeling base sequence effects in double stranded helices.     
Hartmann B, Lavery R
(1989) J Biomol Struct Dyn 7 : 363-80

82.  Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix: "curves", dials and windows.     
Ravishanker G, Swaminathan S, Beveridge DL, Lavery R, Sklenar H
(1989) J Biomol Struct Dyn 6 : 669-99

81.  Defining the structure of irregular nucleic acids: conventions and principles.     
Lavery R, Sklenar H
(1989) J Biomol Struct Dyn 6 : 655-67

80.  Theoretical prediction of base sequence effects in DNA. Experimental reactivity of Z-DNA and B-Z transition enthalpies.     
Hartmann B, Malfoy B, Lavery R
(1989) J Mol Biol 207 : 433-44

79.  Modelling basic features of specificity in DNA-aureolic acid-derived antibiotic interactions.   
Chen KX, Gresh N, Hui X, Pullman B, Zakrzewska K
(1989) FEBS Lett 245 : 145-9

78.  Theoretical modeling of DNA-monocationic lexitropsin complexation: influence of ligand binding on DNA curvature.     
Randrianarivelo M, Zakrzewska K, Pullman B
(1989) J Biomol Struct Dyn 6 : 769-79

1988 [Top] 6
77.  The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids.     
Lavery R, Sklenar H
(1988) J Biomol Struct Dyn 6 : 63-91

76.  Energetic coupling between DNA bending and base pair opening.     
Ramstein J, Lavery R
(1988) Proc Natl Acad Sci U S A 85 : 7231-5

75.  Theoretical study of the sequence selectivity of isolexins, isohelical DNA groove binding ligands. Proposal for the GC minor groove specific compounds.     
Zakrzewska K, Pullman B
(1988) J Biomol Struct Dyn 5 : 1043-58

74.  Sequence-targeted cleavage of nucleic acids by oligo-alpha-thymidylate-phenanthroline conjugates: parallel and antiparallel double helices are formed with DNA and RNA, respectively.     
Sun JS, Francois JC, Lavery R, Saison-Behmoaras T, Montenay-Garestier T, Thuong NT, Helene C
(1988) Biochemistry 27 : 6039-45

73.  Drug recognition of DNA. Proposal for GC minor groove specific ligands: vinylexins.     
Zakrzewska K, Randrianarivelo M, Pullman B
(1988) J Biomol Struct Dyn 6 : 331-44

72.  DNA stem-loop structures in oligopurine-oligopyrimidine triplexes.     
Harvey SC, Luo J, Lavery R
(1988) Nucleic Acids Res 16 : 11795-809

1987 [Top] 4
71.  Theoretical study of the sequence specificity in the covalent binding of the antitumor drug CC-1065 to DNA.     
Zakrzewska K, Randrianarivelo M, Pullman B
(1987) Nucleic Acids Res 15 : 5775-85

70.  A theoretical study of the sequence specificity in binding of lexitropsins to B-DNA.     
Zakrzewska K, Lavery R, Pullman B
(1987) J Biomol Struct Dyn 4 : 833-43

69.  In vitro metabolism of androstenedione and identification of endogenous steroids in Helix aspersa.     
Le Guellec D, Thiard MC, Remy-Martin JP, Deray A, Gomot L, Adessi GL
(1987) Gen Comp Endocrinol 66 : 425-33

68.  Sequence selectivity, a test of the nature of the covalent adduct formed between benzo[a]pyrene and DNA.     
Zakrzewska K, Pullman B
(1987) J Biomol Struct Dyn 4 : 845-58

1986 [Top] 10
67.  The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA.     
Lavery R, Sklenar H, Zakrzewska K, Pullman B
(1986) J Biomol Struct Dyn 3 : 989-1014

66.  The flexibility of the nucleic acids: (I). "SIR", a novel approach to the variation of polymer geometry in constrained systems.     
Sklenar H, Lavery R, Pullman B
(1986) J Biomol Struct Dyn 3 : 967-87

65.  The flexibility of the nucleic acids: (III). The interaction of an aliphatic diamine, putrescine, with flexible B-DNA.     
Lavery R, Sklenar H, Pullman B
(1986) J Biomol Struct Dyn 3 : 1015-31

64.  Guanine and 7-methylguanine amino proton exchange rates as a function of buffer pK: implications for the exchange mechanism.     
Hartmann B, Lavery R, Ramstein J
(1986) Nucleic Acids Res 14 : 7083-92

63.  Theoretical studies on the interaction of proteins and nucleic acids. I. The binding of beta-pleated sheets to A- and B-DNA.     
Zakrzewska K, Pullman B
(1986) Biophys Chem 23 : 251-9

62.  A general approach to the optimization of the conformation of ring molecules with an application to valinomycin.     
Lavery R, Parker I, Kendrick J
(1986) J Biomol Struct Dyn 4 : 443-62

61.  Spermine-nucleic acid interactions: a theoretical study.     
Zakrzewska K, Pullman B
(1986) Biopolymers 25 : 375-92

60.  Theoretical studies on the interaction of proteins and nucleic acid. II. The binding of alpha-helix to B-DNA.     
Zakrzewska K, Lavery R, Pullman B
(1986) Biophys Chem 25 : 201-13

59.  Binding of non-intercalating antibiotics to B-DNA: a theoretical study taking into account nucleic acid flexibility.     
Lavery R, Zakrzewska K, Pullman B
(1986) J Biomol Struct Dyn 3 : 1155-70

58.  A theoretical investigation of the sequence specificity in the binding of the antitumor drug anthramycin to DNA.     
Zakrzewska K, Pullman B
(1986) J Biomol Struct Dyn 4 : 127-36

1985 [Top] 5
57.  The dependence of the surface electrostatic potential of B-DNA on environmental factors.     
Lavery R, Pullman B
(1985) J Biomol Struct Dyn 2 : 1021-32

56.  Theoretical exploration of netropsin binding to tRNA(Phe).     
Zakrzewska K, Pullman B
(1985) J Biomol Struct Dyn 2 : 737-43

55.  Studies of the dependence of the internal energy of DNA on its conformation.   
Lavery R, Sklenar H
(1985) Prog Clin Biol Res 172B : 3-13

54.  The effect of spermine binding on the reactivity of DNA towards carcinogenic alkylating agents.     
Zakrzewska K, Pullman B
(1985) J Biomol Struct Dyn 3 : 437-44

53.  OPTIMIZED MONOPOLE EXPANSIONS FOR THE REPRESENTATION OF THE ELECTROSTATIC PROPERTIES OF POLYPEPTIDES AND PROTEINS      
ZAKRZEWSKA K, PULLMAN A
(1985) JOURNAL OF COMPUTATIONAL CHEMISTRY  6 : 265-273

1984 [Top] 6
52.  A new theoretical index of biochemical reactivity combining steric and electrostatic factors. An application to yeast tRNAPhe.     
Lavery R, Pullman A
(1984) Biophys Chem 19 : 171-81

51.  The solvation contribution to the binding energy of DNA with non-intercalating antibiotics.     
Zakrzewska K, Lavery R, Pullman B
(1984) Nucleic Acids Res 12 : 6559-74

50.  EFFECT OF NUCLEIC-ACID FLEXIBILITY UPON ASIF (ACCESSIBLE SURFACE INTEGRATED FIELD) - POSSIBLE SIGNIFICANCE FOR BIOCHEMICAL REACTIVITY EXEMPLIFIED BY AFLATOXIN-B1 BINDING      
FUROISCORBIN S, PULLMAN B, LAVERY R
(1984) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  Suppl. 11 : 273-286

49.  THE MECHANISM OF INTERACTION OF NON-INTERCALATING GROOVE BINDING LIGANDS WITH DNA      
ZAKRZEWSKA K, PULLMAN B
(1984) STUDIA BIOPHYSICA  104 : 255-256

48.  OPTIMIZED MONOPOLE EXPANSIONS FOR THE REPRESENTATION OF THE ELECTROSTATIC PROPERTIES OF THE NUCLEIC-ACIDS      
LAVERY R, ZAKRZEWSKA K, PULLMAN A
(1984) JOURNAL OF COMPUTATIONAL CHEMISTRY  5 : 363-373

47.  THE INFLUENCE OF NETROPSIN BINDING ON THE STRUCTURE OF DNA      
LAVERY R, SKELNAR H, PULLMAN B
(1984) STUDIA BIOPHYSICA  104 : 285-290

1983 [Top] 6
46.  MOLECULAR ELECTROSTATIC POTENTIAL OF A TRIPLE STRANDED HELIX - POLY(DT).POLY(DA).POLY(DT)      
CORBIN S, LAVERY R, PULLMAN B
(1983) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  23 : 1451-1461

45.  A theoretical evaluation of the effect of netropsin binding on the reactivity of DNA towards alkylating agents.     
Zakrzewska K, Pullman B
(1983) Nucleic Acids Res 11 : 8841-5

44.  Theoretical studies of the selective binding to DNA of two non-intercalating ligands: netropsin and SN 18071.     
Zakrzewska K, Lavery R, Pullman B
(1983) Nucleic Acids Res 11 : 8825-39

43.  MOLECULAR ELECTROSTATIC POTENTIAL VERSUS FIELD - SIGNIFICANCE FOR DNA AND ITS CONSTITUENTS      
PULLMAN A, PULLMAN B, LAVERY R
(1983) THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE  10 : 85-91

42.  ON THE ELECTROSTATIC PROPERTIES OF PAPAIN IN RELATION TO ITS ENZYMATIC-ACTIVITY      
LAVERY R, PULLMAN A, WEN YK
(1983) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  24 : 353-371

41.  The electrostatic field of the component units of DNA and its relationship to hydration.     
Lavery R, Pullman A, Pullman B
(1983) Biophys Chem 17 : 75-86

1982 [Top] 14
40.  THE ELECTROSTATIC-FIELD OF OLIGONUCLEOTIDES - RELATIONSHIP TO HYDRATION      
LAVERY R, PULLMAN B
(1982) STUDIA BIOPHYSICA  92 : 99-110

39.  The electrostatic field of DNA: the role of the nucleic acid conformation.     
Lavery R, Pullman B
(1982) Nucleic Acids Res 10 : 4383-95

38.  THE MOLECULAR ELECTROSTATIC POTENTIAL OF DNA - THE EFFECT OF COUNTER-CATION SCREENING ON VARIOUS ALLOMORPHIC FORMS      
CORBIN S, LAVERY R, PULLMAN B
(1982) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  Suppl. 9 : 103-110

37.  THE CALCULATION OF MOLECULAR ELECTROSTATIC POTENTIAL FROM A MULTIPOLE EXPANSION BASED ON LOCALIZED ORBITALS AND DEVELOPED AT THEIR CENTROIDS - ACCURACY AND APPLICABILITY FOR MACROMOLECULAR COMPUTATIONS      
ETCHEBEST C, LAVERY R, PULLMAN A
(1982) THEORETICA CHIMICA ACTA  62 : 17-28

36.  Two aspects of DNA polymorphism and microheterogeneity: molecular electrostatic potential and steric accessibility.     
Pullman B, Lavery R, Pullman A
(1982) Eur J Biochem 124 : 229-38

35.  CALCULATION OF THE MOLECULAR ELECTROSTATIC POTENTIAL FROM A MULTIPOLE EXPANSION BASED ON LOCALIZED ORBITALS      
LAVERY R, ETCHEBEST C, PULLMAN A
(1982) CHEMICAL PHYSICS LETTERS  85 : 266-270

34.  The effects of countercation screening on the electrostatic potential of DNA. The role of the nucleic acid conformation.     
Lavery R, Pullman B
(1982) FEBS Lett 142 : 271-4

33.  MOLECULAR ELECTROSTATIC POTENTIAL AND ATOMIC ACCESSIBILITIES OF THE COMPLEXED AND FREE FORMS OF VALINOMYCIN      
ETCHEBEST C, LAVERY R, PULLMAN A
(1982) STUDIA BIOPHYSICA  90 : 7-15

32.  The molecular electrostatic potential and steric accessibility of double-helical A-RNA.     
Corbin S, Lavery R, Pullman B
(1982) Biochim Biophys Acta 698 : 86-92

31.  THE MOLECULAR ELECTROSTATIC POTENTIAL AND STERIC ACCESSIBILITY OF C-DNA      
LAVERY R, CORBIN S, PULLMAN B
(1982) THEORETICA CHIMICA ACTA  60 : 513-522

30.  THE ELECTROSTATIC-FIELD OF B-DNA      
LAVERY R, PULLMAN A, PULLMAN B
(1982) THEORETICA CHIMICA ACTA  62 : 93-106

29.  ELECTROSTATIC MOLECULAR-POTENTIAL OF PHOSPHOLIPID LAYERS      
PULLMAN B, ZAKRZEWSKA K
(1982) STUDIA BIOPHYSICA  90 : 1-6

28.  THE DEPENDENCE OF THE ELECTROSTATIC PROPERTIES OF MODEL PHOSPHOLIPID MONOLAYERS ON THEIR MOLECULAR-ORGANIZATION      
ZAKRZEWSKA K, PULLMAN A
(1982) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  Suppl. 9 : 411-424

27.  Intrinsic electrostatic properties and base sequence effects in the structure of oligonucleotides.     
Lavery R, Pullman B, Zakrzewska K
(1982) Biophys Chem 15 : 343-51

1981 [Top] 10
26.  THE MOLECULAR ELECTROSTATIC POTENTIAL OF PHOSPHOLIPID MONOLAYERS AND BILAYERS      
ZAKRZEWSKA K, PULLMAN B
(1981) FEBS LETTERS  131 : 77-80

25.  The molecular electrostatic potential and steric accessibility of A-DNA.     
Lavery R, Pullman B
(1981) Nucleic Acids Res 9 : 4677-88

24.  STERIC ACCESSIBILITY OF REACTIVE CENTERS IN B-DNA      
LAVERY R, PULLMAN A, PULLMAN B
(1981) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  20 : 49-62

23.  THE ELECTROSTATIC POTENTIAL OF A MODEL PHOSPHOLIPID MONOLAYER      
ZAKRZEWSKA K, LAVERY R, PULLMAN B
(1981) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  Suppl. 8 : 161-170

22.  The molecular electrostatic potential and steric accessibility of poly (dI.dC). Comparison with poly (dG.dC).     
Lavery R, Pullman B
(1981) Nucleic Acids Res 9 : 7041-51

21.  THE ELECTROSTATIC POTENTIAL OF A MODEL PHOSPHATIDYLCHOLINE MONOLAYER AND BILAYER      
ZAKRZEWSKA K, PULLMAN B
(1981) FEBS LETTERS  135 : 268-272

20.  The molecular electrostatic potential, steric accessibility and hydration of Dickerson's B-DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG).     
Lavery R, Pullman B
(1981) Nucleic Acids Res 9 : 3765-77

19.  THE ELECTROSTATIC MOLECULAR-POTENTIAL OF TRANSFER RNAPHE .5. THE INFLUENCE OF COUNTERION BINDING ON THE POTENTIAL AND THE STERIC ACCESSIBILITY      
LAVERY R, CORBIN S, PULLMAN A
(1981) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  Suppl. 8 : 171-183

18.  MOLECULAR ELECTROSTATIC POTENTIAL ON THE SURFACE ENVELOPES OF MACROMOLECULES - B-DNA      
LAVERY R, PULLMAN B
(1981) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  20 : 259-272

17.  The molecular electrostatic potential and steric accessibility of poly (dA-dT). poly (dA-dT) in various conformations: B-DNA, D-DNA and 'alternating-B' DNA.     
Lavery R, Pullman B, Corbin S
(1981) Nucleic Acids Res 9 : 6539-52

1980 [Top] 7
16.  THE ELECTROSTATIC MOLECULAR-POTENTIAL OF YEAST TRANSFER RNAPHE .3. THE MOLECULAR-POTENTIAL AND THE STERIC ACCESSIBILITY ASSOCIATED WITH THE PHOSPHATE GROUPS      
LAVERY R, PULLMAN A, PULLMAN B
(1980) THEORETICA CHIMICA ACTA  57 : 233-243

15.  THE ELECTROSTATIC POTENTIAL OF YEAST TRANSFER RNAPHE .2. THE POTENTIALS OF THE PHOSPHATE GROUPS IN THEIR VARIOUS CONFORMATIONAL STATES      
LAVERY R, DEOLIVEIRA M, PULLMAN B
(1980) JOURNAL OF COMPUTATIONAL CHEMISTRY  1 : 301-306

14.  The electrostatic molecular potential of yeast tRNAPhe. (I). The potential due to the phosphate backbone.     
Lavery R, Pullman A, Pullman B
(1980) Nucleic Acids Res 8 : 1061-79

13.  MOLECULAR ELECTROSTATIC POTENTIAL OF THE B-DNA HELIX .7. EFFECT OF SCREENING BY MONO-VALENT CATIONS      
LAVERY R, CAUCHY D, DELALUZROJAS O, PULLMAN A
(1980) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  18 : 323-330

12.  THE EFFECT OF SCREENING THE ELECTROSTATIC POTENTIALS OF REACTIVE SITES WITHIN B-DNA BY METAL-CATIONS      
CAUCHY D, LAVERY R, PULLMAN B
(1980) THEORETICA CHIMICA ACTA  57 : 323-327

11.  The electrostatic potential and steric accessibility of reactive sites within Z-DNA.     
Zakrzewska K, Lavery R, Pullman A, Pullman B
(1980) Nucleic Acids Res 8 : 3917-32

10.  The electrostatic molecular potential of tRNAPhe. IV. The potentials and steric accessibilities of sites associated with the bases.     
Lavery R, Pullman A, Pullman B, De Oliveira M
(1980) Nucleic Acids Res 8 : 5095-111

1979 [Top] 4
9.  MOLECULAR ELECTROSTATIC POTENTIAL OF THE B-DNA HELIX .4. C-8 AND AMINO SITES OF PURINES AND THE BINDING OF CARCINOGENIC ACETYLAMINOFLUORENE TO DNA      
LAVERY R, PULLMAN B
(1979) THEORETICA CHIMICA ACTA  53 : 175-181

8.  Affinity labeling of catalytic and regulatory sites of pig heart mitochondrial F1-ATPase by 5'-p-fluorosulfonylbenzoyladenosine.     
Di Pietro A, Godinot C, Martin JC, Gautheron DC
(1979) Biochemistry 18 : 1738-45

7.  MODEL QUANTUM CHEMICAL STUDIES OF THE ELECTRONIC-STRUCTURE AND ASPECTS OF REACTIVITY OF DIOL EPOXIDES OF AROMATIC-HYDROCARBONS      
LAVERY R, PULLMAN B
(1979) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  15 : 271-280

6.  THEORETICAL-MODEL STUDY OF THE REACTIVITY OF BENZO(A)PYRENE DIOL EPOXIDE WITH THE AMINO-GROUPS OF THE NUCLEIC-ACID BASES      
LAVERY R, PULLMAN B
(1979) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  16 : 175-188

1978 [Top] 4
5.  MODEL QUANTUM-CHEMICAL STUDIES ON THE REACTION BETWEEN THE CANDIDATE PROXIMATE CARCINOGEN BENZO(A)PYRENE-7,8-DIHYDRODIOL-9,10-EPOXIDE AND GUANINE      
LAVERY R, PULLMAN A, PULLMAN B
(1978) INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY  Suppl. 5 : 21-34

4.  CLUSTER AND CRYSTAL ORBITAL APPROACHES TO ADSORPTION OF HYDROGEN ON LITHIUM METAL      
LAVERY R, HILLIER IH
(1978) JOURNAL OF MOLECULAR CATALYSIS  4 : 9-20

3.  CRYSTAL ORBITAL STUDIES OF CHEMISORPTION - ADSORPTION ON GRAPHITE AND ALUMINUM      
LAVERY R, HILLIER IH
(1978) JOURNAL OF MOLECULAR CATALYSIS  4 : 299-306

2.  RELATIVE ACIDITY AND BASICITY OF AMINO-GROUPS OF NUCLEIC-ACID BASES      
LAVERY R, PULLMAN A, PULLMAN B
(1978) THEORETICA CHIMICA ACTA  50 : 67-73

1974 [Top] 1
1.  Conformation of nucleosides: circular dichroism study of solvent effect on the syn-anti conformational equilibrium of pyrimidine nucleosides.   
Rabczenko A, Jankowski K, Zakrzewska K
(1974) Biochim Biophys Acta 353 : 1-15