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R. Lavery · SciRah

Researcher profile · Semantic Scholar

R. Lavery

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R. Lavery — researcher profile on SciRah

h-index: 53
Works: 204
Citations: 11K

Most-cited papers

Conformational analysis of nucleic acids revisited: Curves+
R. Lavery, Maher Moakher, J. Maddocks, D. Petkeviciute +1 more
2009Nucleic Acids Research733 citations Open access
Semantic Scholar
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
R. Lavery, K. Zakrzewska, D. Beveridge, T. Bishop +14 more
2009Nucleic Acids Research321 citations Open access
Semantic Scholar
Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.
J. Bednar, I. Garcia-Saez, R. Boopathi, Amber R. Cutter +17 more
2017Molecules and Cells269 citations Open access
Semantic Scholar
CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures
Christophe Blanchet, M. Pasi, K. Zakrzewska, R. Lavery
2011Nucleic Acids Res.245 citations Open access
Semantic Scholar
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps.
D. Beveridge, G. Barreiro, K. Byun, D. Case +13 more
2004Biophysical Journal245 citations Open access
Semantic Scholar
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.
S. Dixit, D. Beveridge, D. Case, T. Cheatham +8 more
2005Biophysical Journal233 citations Open access
Semantic Scholar
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
M. Pasi, J. Maddocks, D. Beveridge, T. Bishop +15 more
2014Nucleic Acids Research202 citations Open access
Semantic Scholar
On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes.
A. Mukherjee, R. Lavery, B. Bagchi, J. Hynes
2008Journal of the American Chemical Society172 citations
Semantic Scholar
Kinking occurs during molecular dynamics simulations of small DNA minicircles.
F. Lankaš, R. Lavery, J. Maddocks
2006Structure169 citations Open access
Semantic Scholar
Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.
Emmanuel Giudice, P. Várnai, R. Lavery
2003Nucleic Acids Research146 citations Open access
Semantic Scholar
Wringing out DNA.
T. Lionnet, S. Joubaud, R. Lavery, D. Bensimon +1 more
2006Physical Review Letters144 citations Open access
Semantic Scholar
Analyzing protein-DNA recognition mechanisms.
G. Paillard, R. Lavery
2004Structure112 citations Open access
Semantic Scholar
Structure and mechanics of single biomolecules: experiment and simulation
R. Lavery, A. Lebrun, J. Allemand, D. Bensimon +1 more
2002109 citations
Semantic Scholar
Analyzing ion distributions around DNA
R. Lavery, J. Maddocks, M. Pasi, K. Zakrzewska
2014Nucleic Acids Research108 citations Open access
Semantic Scholar
Long-timescale dynamics of the Drew–Dickerson dodecamer
P. Dans, L. Danilāne, Iván Ivani, Tomáš Dršata +8 more
2016Nucleic Acids Research99 citations Open access
Semantic Scholar
Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics
M. Pasi, J. Maddocks, R. Lavery
2015Nucleic Acids Research99 citations Open access
Semantic Scholar
Influence of conformational dynamics on the exciton states of DNA oligomers
B. Bouvier, J. Dognon, R. Lavery, D. Markovitsi +3 more
200397 citations
Semantic Scholar
Exploring polymorphisms in B-DNA helical conformations
P. Dans, Alberto Pérez, I. Faustino, R. Lavery +1 more
2012Nucleic Acids Research90 citations Open access
Semantic Scholar
Locating the active sites of enzymes using mechanical properties
S. Sacquin-Mora, É. Laforet, R. Lavery
2007Proteins: Structure, Function, and Bioinformatics87 citations
Semantic Scholar
Cadherin mechanics and complexation: the importance of calcium binding.
Fabien Cailliez, R. Lavery
2005Biophysical Journal85 citations Open access
Semantic Scholar
Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA.
Matthieu Wilhelm, A. Mukherjee, B. Bouvier, K. Zakrzewska +2 more
2012Journal of the American Chemical Society84 citations Open access
Semantic Scholar
Investigating the local flexibility of functional residues in hemoproteins.
S. Sacquin-Mora, R. Lavery
2006Biophysical Journal83 citations Open access
Semantic Scholar
Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling
S. Engelen, L. Trojan, S. Sacquin-Mora, R. Lavery +1 more
2009PLoS Comput. Biol.81 citations Open access
Semantic Scholar
Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA
P. Dans, I. Faustino, F. Battistini, K. Zakrzewska +2 more
2014Nucleic Acids Research79 citations Open access
Semantic Scholar
Local and global effects of strong DNA bending induced during molecular dynamics simulations
J. Curuksu, M. Zacharias, R. Lavery, K. Zakrzewska
2009Nucleic Acids Research76 citations Open access
Semantic Scholar
Non-additivity in protein-DNA binding
R. O'Flanagan, G. Paillard, R. Lavery, Anirvan M. Sengupta
2005Bioinform.68 citations Open access
Semantic Scholar
Protein mechanics: a route from structure to function
R. Lavery, S. Sacquin-Mora
2007Journal of Biosciences65 citations
Semantic Scholar
Exciton states of dynamic DNA double helices: alternating dCdG sequences.
E. Emanuele, K. Zakrzewska, D. Markovitsi, R. Lavery +1 more
2005Journal of Physical Chemistry B64 citations Open access
Semantic Scholar
Identification of protein interaction partners and protein-protein interaction sites.
S. Sacquin-Mora, A. Carbone, R. Lavery
2008Journal of Molecular Biology59 citations
Semantic Scholar
PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.
M. Pasi, R. Lavery, N. Ceres
2013Journal of Chemical Theory and Computation54 citations
Semantic Scholar
Probing the flexibility of the bacterial reaction center: the wild-type protein is more rigid than two site-specific mutants.
S. Sacquin-Mora, P. Sebban, Valérie Derrien, B. Frick +2 more
2007Biochemistry54 citations
Semantic Scholar
Dynamics and recognition within a protein–DNA complex: a molecular dynamics study of the SKN-1/DNA interaction
L. Etheve, Juliette Martin, R. Lavery
2015Nucleic Acids Research53 citations Open access
Semantic Scholar
Protein-DNA recognition triggered by a DNA conformational switch.
B. Bouvier, K. Zakrzewska, R. Lavery
2011Angewandte Chemie53 citations Open access
Semantic Scholar
Myosin flexibility: Structural domains and collective vibrations
Isabelle Navizet, R. Lavery, Robert L. Jernigan
2004Proteins: Structure, Function, and Bioinformatics52 citations Open access
Semantic Scholar
The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules
P. Dans, Alexandra Balaceanu, M. Pasi, A. Patelli +7 more
2019Nucleic Acids Research50 citations Open access
Semantic Scholar
Deforming DNA: from physics to biology.
Chantal Prévost, Masayuki Takahashi, R. Lavery
2009ChemPhysChem48 citations
Semantic Scholar
Protein–DNA interfaces: a molecular dynamics analysis of time-dependent recognition processes for three transcription factors
L. Etheve, Juliette Martin, R. Lavery
2016Nucleic Acids Research46 citations Open access
Semantic Scholar
Significance of Molecular Dynamics Simulations for Life Sciences
M. Karplus, R. Lavery
201444 citations
Semantic Scholar
Probing protein mechanics: residue-level properties and their use in defining domains.
Isabelle Navizet, Fabien Cailliez, R. Lavery
2004Biophysical Journal43 citations Open access
Semantic Scholar
Sequence-dependent response of DNA to torsional stress: a potential biological regulation mechanism
A. Reymer, K. Zakrzewska, R. Lavery
2017Nucleic Acids Research42 citations Open access
Semantic Scholar
Looking into DNA recognition: zinc finger binding specificity.
G. Paillard, C. Deremble, R. Lavery
2004Nucleic Acids Research41 citations Open access
Semantic Scholar
Docking macromolecules with flexible segments
K. Bastard, A. Thureau, R. Lavery, Chantal Prévost
2003Journal of Computational Chemistry41 citations
Semantic Scholar
Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.
Emmanuel Giudice, R. Lavery
2003Journal of the American Chemical Society41 citations
Semantic Scholar
Temperature dependence of the DNA double helix at the nanoscale: structure, elasticity, and fluctuations.
Sam Meyer, D. Jost, N. Theodorakopoulos, M. Peyrard +2 more
2013Biophysical Journal40 citations Open access
Semantic Scholar
Macromolecular recognition.
C. Deremble, R. Lavery
2005Current Opinion in Structural Biology39 citations
Semantic Scholar
Arbitrary protein−protein docking targets biologically relevant interfaces
Juliette Martin, R. Lavery
2012BMC Biophysics36 citations Open access
Semantic Scholar
Dynamics and stability of E-cadherin dimers.
Fabien Cailliez, R. Lavery
2006Biophysical Journal36 citations Open access
Semantic Scholar
Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.
Marie-Pierre Durrieu, P. Bond, M. Sansom, R. Lavery +1 more
2009ChemPhysChem31 citations
Semantic Scholar
Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics
M. Pasi, R. Lavery
2016Nucleic Acids Research30 citations Open access
Semantic Scholar
Interactions between neuronal fusion proteins explored by molecular dynamics.
Marie-Pierre Durrieu, R. Lavery, M. Baaden
2008Biophysical Journal30 citations Open access
Semantic Scholar

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