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

Publications

[2016] [2015] [2014] [2013] [2012] [2011] [2010
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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 44 : 9990-10002

358.  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

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.  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

2015 [Top] 7
355.  Internal Normal Mode Analysis (iNMA) Applied to Protein Conformational Flexibility.   
Frezza E, Lavery R
(2015) J Chem Theory Comput 11 : 5503-12

354.  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

353.  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

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

351.  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

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

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

2014 [Top] 21
348.  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

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

346.  ?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

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

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

342.  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

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

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

339.  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

338.  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

337.  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

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

335.  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

334.  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

333.  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

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

331.  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

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 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

328.  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

2013 [Top] 10
327.  Interaction of pristine and functionalized carbon nanotubes with lipid membranes.   
Baoukina S, Monticelli L, Tieleman DP
(2013) J Phys Chem B 117 : 12113-23

326.  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

325.  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

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

323.  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

322.  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

321.  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

320.  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

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

318.  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

2012 [Top] 14
317.  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

316.  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

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

314.  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

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

312.  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

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

310.  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

309.  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

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

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

306.  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

305.  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

304.  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

2011 [Top] 6
303.  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

302.  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

301.  [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

300.  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

299.  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

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

2010 [Top] 12
297.  Membrane protein dynamics from femtoseconds to seconds   
Kandt C, Monticelli L
(2010) Methods Mol Biol 654 : 423-440

296.  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

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.  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

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.  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

291.  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

290.  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

289.  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

288.  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

287.  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

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

2009 [Top] 14
285.  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

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

283.  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

282.  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

281.  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

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.  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

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

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

276.  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

275.  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

274.  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

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

272.  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

2008 [Top] 18
271.  Identification of protein interaction partners and protein-protein interaction sites.     
Sacquin-Mora S, Carbone A, Lavery R
(2008) J Mol Biol 382 : 1276-89

270.  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

269.  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

268.  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

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

265.  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

264.  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

263.  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

262.  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

261.  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

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

259.  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

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.  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

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

254.  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

2007 [Top] 10
253.  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

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

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

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

249.  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

248.  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

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

246.  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

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

244.  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

2006 [Top] 15
243.  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

242.  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

241.  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

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

239.  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

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

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

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

235.  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

234.  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

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

232.  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

231.  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

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

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.  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

227.  Recognizing DNA.     
Lavery R
(2005) Q Rev Biophys 38 : 339-44

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

225.  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

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

223.  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

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

221.  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

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

219.  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

218.  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

217.  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

216.  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

215.  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

2004 [Top] 16
214.  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

213.  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

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

211.  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

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

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

208.  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

207.  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

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

205.  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

204.  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

203.  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

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

201.  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

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

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

2003 [Top] 10
198.  DNA deformation energetics and protein binding.     
Zakrzewska K
(2003) Biopolymers 70 : 414-23

197.  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

196.  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

195.  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

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

193.  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

192.  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

191.  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

190.  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

189.  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

2002 [Top] 14
188.  Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.     
Varnai P, Lavery R
(2002) J Am Chem Soc 124 : 7272-3

187.  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

186.  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

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

184.  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

183.  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

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

181.  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

180.  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

179.  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

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

177.  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

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

175.  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

2001 [Top] 10
174.  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

173.  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

172.  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

171.  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

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

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

168.  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-

167.  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

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

165.  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

2000 [Top] 9
164.  NPS@: network protein sequence analysis.     
Combet C, Blanchet C, Geourjon C, Deleage G
(2000) Trends Biochem Sci 25 : 147-50

163.  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

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

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

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

159.  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

158.  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

157.  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

156.  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

1999 [Top] 15
155.  Unraveling proteins: a molecular mechanics study.     
Rohs R, Etchebest C, Lavery R
(1999) Biophys J 76 : 2760-8

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

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

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

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

150.  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

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.  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

146.  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

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

144.  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

143.  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

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

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

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

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

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.  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

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

1997 [Top] 9
132.  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

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

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

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

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.  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

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

124.  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

1996 [Top] 5
123.  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

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

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

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

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

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

115.  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

1994 [Top] 5
114.  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

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

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

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

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

1993 [Top] 10
109.  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

108.  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

107.  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

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

105.  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

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

103.  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

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

101.  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

100.  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

1992 [Top] 7
99.  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

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

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

96.  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

95.  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

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

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

1991 [Top] 6
92.  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

91.  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

90.  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

89.  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

88.  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

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

85.  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

1989 [Top] 7
84.  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

83.  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

82.  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

81.  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

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

79.  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

78.  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

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.  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

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

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

72.  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

1987 [Top] 4
71.  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

70.  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

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.  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

1986 [Top] 10
67.  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

66.  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

65.  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

64.  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

63.  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

62.  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

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

60.  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

59.  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

58.  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

1985 [Top] 5
57.  Theoretical exploration of netropsin binding to tRNA(Phe).     
Zakrzewska K, Pullman B
(1985) J Biomol Struct Dyn 2 : 737-43

56.  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

55.  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

54.  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

53.  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

1984 [Top] 6
52.  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

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

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

49.  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

48.  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

47.  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

1983 [Top] 6
46.  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

45.  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

44.  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

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.  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

41.  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

1982 [Top] 14
40.  THE MOLECULAR ELECTROSTATIC POTENTIAL AND STERIC ACCESSIBILITY OF C-DNA      
LAVERY R, CORBIN S, PULLMAN B
(1982) THEORETICA CHIMICA ACTA  60 : 513-522

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

37.  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

36.  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

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

34.  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

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

32.  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

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

30.  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

29.  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

28.  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

27.  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

1981 [Top] 10
26.  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

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

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

23.  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

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

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

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

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.  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

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

1980 [Top] 7
16.  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

15.  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

14.  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

13.  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

12.  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

11.  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

10.  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

1979 [Top] 4
9.  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

8.  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

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.  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

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

4.  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

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