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Richard LAVERY



Equipe/Team : Bioinformatique Structures et Interactions (BISI)
Courriel/Mail : This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Téléphone/Phone : +33(0)4-72-72-26-37
Fax/Fax : +33(0)4-72-72-26-04
Statut/Status : Directeur de recherches

Webpage : http://perso.ibcp.fr/richard.lavery/



198 Publications/Papers :
[2017] [2016] [2015] [2014] [2013] [2012] [2011] [2010
[2009] [2008] [2007] [2006] [2005] [2004] [2003] [2002] [2001] [2000
[1999] [1998] [1997] [1996] [1995] [1994] [1993] [1992] [1991] [1990
[1989] [1988] [1987] [1986] [1985] [1984] [1983] [1982] [1981] [1980
[1979] [1978

2017 [Top] 1
198.  Analyzing DNA curvature and its impact on the ionic environment: application to molecular dynamics simulations of minicircles.   
Pasi M, Zakrzewska K, Maddocks JH, Lavery R
(2017) Nucleic Acids Res 

2016 [Top] 2
197.  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

196.  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

2015 [Top] 2
195.  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

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

2014 [Top] 3
193.  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

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

191.  ?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

2013 [Top] 1
190.  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] 5
189.  A Protein Solvation Model Based on Residue Burial   
Ceres N, Pasi M, Lavery R
(2012) JOURNAL OF CHEMICAL THEORY AND COMPUTATION  8 : 2141-2144

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

187.  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

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

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

2011 [Top] 2
184.  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

183.  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] 1
182.  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

2009 [Top] 9
181.  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

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

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

178.  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

177.  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

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

175.  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

174.  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

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

2008 [Top] 5
172.  Protein-DNA recognition: Breaking the combinatorial barrier     
Deremble C, Lavery R, Zakrzewska K
(2008) COMPUTER PHYSICS COMMUNICATIONS 179 : 112-119

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

170.  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

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

168.  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

2007 [Top] 5
167.  Theory and simulation     
Lavery R , Sharp KA
(2007) CURRENT OPINION IN STRUCTURAL BIOLOGY 17 : 147-148

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

165.  Probing macromolecular mechanics: Heterogeneity and function     
Lavery R , Sacquin-Mora S
(2007) JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 24 : 763-763

164.  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

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

2006 [Top] 5
162.  Wringing out DNA.     
Lionnet T, Joubaud S, Lavery R, Bensimon D, Croquette V
(2006) Phys Rev Lett 96 : 178102-178102

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

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

159.  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

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

2005 [Top] 7
157.  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

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

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

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

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

152.  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

151.  Molecular modeling of the low density lipoprotein receptor mutations responsible for familial hypercholesterolemia in Morocco      
Kettani A, Ymlahi Q, Chater R, Chihab KA, Moussamih S, Bennis F, Adlouni A, Zakrewska K, Lavery R, Perahia D, El Messal M
(2005) ATHEROSCLEROSIS SUPPLEMENTS  6 : 172-172

2004 [Top] 6
150.  Probing protein mechanics: residue-level properties and their use in defining domains.     
Navizet I, Cailliez F, Lavery R
(2004) Biophys J 87 : 1426-35

149.  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

148.  Analyzing protein-DNA recognition.      
Lavery R, Paillard G
(2004) ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  227 : U914-U914

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

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

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

2003 [Top] 5
144.  Docking macromolecules with flexible segments.     
Bastard K, Thureau A, Lavery R, Prevost C
(2003) J Comput Chem 24 : 1910-20

143.  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

142.  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

141.  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

140.  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

2002 [Top] 5
139.  Simulations of nucleic acids and their complexes.     
Giudice E, Lavery R
(2002) Acc Chem Res 35 : 350-7

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

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

136.  Base flipping in DNA double helix.      
Varnai P, Giudice E, Lavery R
(2002) ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  223 : U499-U499

135.  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] 4
134.  Symposium proceedings: Computational Biophys 2000 - Preface      
Lavery R, Richards G
(2001) THEORETICAL CHEMISTRY ACCOUNTS  106 : 1-1

133.  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

132.  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-

131.  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] 6
130.  ADAPT: a molecular mechanics approach for studying the structural properties of long DNA sequences.     
Lafontaine I, Lavery R
(2000) Biopolymers 56 : 292-310

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

128.  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

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

126.  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

125.  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

1999 [Top] 12
124.  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

123.  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

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

121.  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

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

119.  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

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

117.  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

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

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

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

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

1998 [Top] 5
112.  Thoughts on physical chemistry      
Markovitsi D, Lavery R
(1998) ACTUALITE CHIMIQUE   : 26-27

111.  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

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

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

108.  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] 7
107.  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

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

105.  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

104.  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

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

102.  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

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

1996 [Top] 5
100.  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

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

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

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

96.  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
95.  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

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

93.  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

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

1994 [Top] 4
91.  Measuring the geometry of DNA grooves.     
Stofer E, Lavery R
(1994) Biopolymers 34 : 337-46

90.  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

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

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

1993 [Top] 9
87.  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

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

85.  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

84.  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

83.  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

82.  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

81.  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

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

79.  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] 6
78.  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

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

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

75.  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

74.  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

73.  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
72.  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

71.  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

70.  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

69.  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

68.  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

67.  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
66.  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

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

1989 [Top] 6
64.  MODELING AND MEASURING DNA DEFORMATION      
LAVERY R
(1989) JOURNAL OF MOLECULAR GRAPHICS  7 : 179-179

63.  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

62.  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

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

60.  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

59.  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

1988 [Top] 4
58.  Energetic coupling between DNA bending and base pair opening.     
Ramstein J, Lavery R
(1988) Proc Natl Acad Sci U S A 85 : 7231-5

57.  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

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

55.  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

1987 [Top] 1
54.  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] 7
53.  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

52.  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

51.  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

50.  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

49.  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

48.  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

47.  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] 2
46.  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

45.  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

1984 [Top] 5
44.  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

43.  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

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

41.  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

40.  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

1983 [Top] 5
39.  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

38.  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

37.  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

36.  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

35.  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

1982 [Top] 12
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.  The electrostatic field of DNA: the role of the nucleic acid conformation.     
Lavery R, Pullman B
(1982) Nucleic Acids Res 10 : 4383-95

32.  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

31.  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

30.  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

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

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

27.  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

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

25.  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

24.  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

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

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

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

19.  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

18.  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

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

16.  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

15.  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
14.  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

13.  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

12.  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

11.  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

10.  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

9.  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

8.  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] 3
7.  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

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

5.  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

1978 [Top] 4
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.  RELATIVE ACIDITY AND BASICITY OF AMINO-GROUPS OF NUCLEIC-ACID BASES      
LAVERY R, PULLMAN A, PULLMAN B
(1978) THEORETICA CHIMICA ACTA  50 : 67-73

2.  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

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