Richard Lavery

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John H. MaddocksProfessor of Mathematics, EPFLVerified email at epfl.ch
Marco PasiLaboratoire de Biologie et Pharmacologie Appliquée - ENS Paris-SaclayVerified email at ens-paris-saclay.fr
David BensimonEcole Normale SupérieureVerified email at lps.ens.fr
Peter VarnaiTechnopolis GroupVerified email at technopolis-group.com
emmanuel giudiceMaître de Conférences, UMR CNRS 6290, University of Rennes 1Verified email at univ-rennes1.fr
Modesto OrozcoProfessor of Biochemistry, Universtity of Barcelona and Group Leader IRB BarcelonaVerified email at irbbarcelona.org
David A CaseRutgers UniversityVerified email at biomaps.rutgers.edu
Sophie Sacquin-MoraLab. Biochimie Théorique-CNRS Paris, @sacquin_mo@fediscience.org, https://topoftheprots.com/Verified email at ibpc.fr
Thomas E. Cheatham, IIIProfessor of Medicinal Chemistry; Director Research Computing; University of UtahVerified email at utah.edu
Prévost ChantalResearcher CNRSVerified email at ibpc.fr
Pablo D. DansDepartment of Biological Sciences (CENUR Litoral Norte - UdelaR) & Institut Pasteur de MontevideoVerified email at pasteur.edu.uy
jean louis viovyCNRS; Institut Curie; Institut Pierre Gilles de Gennes IPGG; FluigentVerified email at curie.fr
Alberto PerezUniversity of Florida, Department of ChemistryVerified email at chem.ufl.edu
Dimitra MarkovitsiCNRS Emeritus Research DirectorVerified email at universite-paris-saclay.fr
Arnab MukherjeeIISER PuneVerified email at iiserpune.ac.in
Juliette MartinLaboratoire de Biologie et Modélisation de la Cellule - CNRS UMR 5239 - Inserm 1293 - ENS LyonVerified email at ens-lyon.fr
Matthew A. YoungUniversity of MichiganVerified email at umich.edu
B. JayaramSupercomputing Facility for Bioinformatics & Computational Biology, IIT DelhiVerified email at chemistry.iitd.ac.in
Stephen C HarveyDepartment of Biochemistry & Biophysics, University of PennsylvaniaVerified email at mail.med.upenn.edu
Fabien CailliezICP - Université Paris-SaclayVerified email at universite-paris-saclay.fr

Richard Lavery

IBCP, CNRS / University of Lyon

Verified email at ibcp.fr - Homepage

Molecular modeling and simulation


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DNA: an extensible molecule P Cluzel, A Lebrun, C Heller, R Lavery, JL Viovy, D Chatenay, F Caron Science 271 (5250), 792-794, 1996	1354	1996
The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids R Lavery, H Sklenar Journal of Biomolecular Structure and Dynamics 6 (1), 63-91, 1988	1124	1988
Defining the structure of irregular nucleic acids: conventions and principles R Lavery, H Sklenar Journal of Biomolecular Structure and Dynamics 6 (4), 655-667, 1989	897	1989
Conformational analysis of nucleic acids revisited: Curves+ R Lavery, M Moakher, JH Maddocks, D Petkeviciute, K Zakrzewska Nucleic acids research 37 (17), 5917-5929, 2009	783	2009
Stretched and overwound DNA forms a Pauling-like structure with exposed bases JF Allemand, D Bensimon, R Lavery, V Croquette Proceedings of the National Academy of Sciences 95 (24), 14152-14157, 1998	498	1998
A new approach to the rapid determination of protein side chain conformations P Tuffery, C Etchebest, S Hazout, R Lavery Journal of Biomolecular structure and dynamics 8 (6), 1267-1289, 1991	442	1991
Energetic coupling between DNA bending and base pair opening. J Ramstein, R Lavery Proceedings of the National Academy of Sciences 85 (19), 7231-7235, 1988	389	1988
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, TC Bishop, DA Case, ... Nucleic acids research 38 (1), 299-313, 2010	356	2010
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d (CpG) steps DL Beveridge, G Barreiro, KS Byun, DA Case, TE Cheatham, SB Dixit, ... Biophysical journal 87 (6), 3799-3813, 2004	327	2004
Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1 J Bednar, I Garcia-Saez, R Boopathi, AR Cutter, G Papai, A Reymer, ... Molecular cell 66 (3), 384-397. e8, 2017	318	2017
Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d (CGCGAATTCGCG) double helix:“curves”, dials and windows G Ravishanker, S Swaminathan, DL Beveridge, R Lavery, H Sklenar Journal of Biomolecular Structure and Dynamics 6 (4), 669-699, 1989	309	1989
Modelling extreme stretching of DNA A Lebrun, R Lavery Nucleic acids research 24 (12), 2260-2267, 1996	284	1996
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique … SB Dixit, DL Beveridge, DA Case, TE Cheatham, E Giudice, F Lankas, ... Biophysical journal 89 (6), 3721-3740, 2005	278	2005
CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures C Blanchet, M Pasi, K Zakrzewska, R Lavery Nucleic acids research 39 (suppl_2), W68-W73, 2011	243	2011
JUMNA (junction minimisation of nucleic acids) R Lavery, K Zakrzewska, H Sklenar Computer Physics Communications 91 (1-3), 135-158, 1995	233	1995
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA M Pasi, JH Maddocks, D Beveridge, TC Bishop, DA Case, T Cheatham III, ... Nucleic acids research 42 (19), 12272-12283, 2014	223	2014
Methylene blue binding to DNA with alternating GC base sequence: a modeling study R Rohs, H Sklenar, R Lavery, B Röder Journal of the American Chemical Society 122 (12), 2860-2866, 2000	215	2000
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, JT Hynes Journal of the American Chemical Society 130 (30), 9747-9755, 2008	212	2008
Kinking occurs during molecular dynamics simulations of small DNA minicircles F Lankaš, R Lavery, JH Maddocks Structure 14 (10), 1527-1534, 2006	200	2006
Wringing out DNA T Lionnet, S Joubaud, R Lavery, D Bensimon, V Croquette Physical Review Letters 96 (17), 178102, 2006	200	2006

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