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List of works by Richard Lavery

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DNA: an extensible molecule

scientific article
Conformational analysis of nucleic acids revisited: Curves+

scientific article (publication date: September 2009)
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

scientific article
Stretched and overwound DNA forms a Pauling-like structure with exposed bases

scientific article
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

scientific article
Modelling extreme stretching of DNA.

scientific article published on June 1996
CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

scientific article
Kinking occurs during molecular dynamics simulations of small DNA minicircles

scientific article published in October 2006
μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

scientific article
Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

scientific article
Analyzing protein-DNA recognition mechanisms

scientific article published in January 2004
Measuring the geometry of DNA grooves

scientific article published in March 1994
Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling

scientific article
Local DNA stretching mimics the distortion caused by the TATA box-binding protein

scientific article
On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes

scientific article
Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis.

scientific article
Exploring polymorphisms in B-DNA helical conformations.

scientific article published on 24 September 2012
Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

scientific article
Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics.

scientific article
Wringing out DNA

scientific article published on 05 May 2006
Conformational sub-states in B-DNA.

scientific article published in August 1992
Analyzing ion distributions around DNA.

scientific article
Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature.

scientific article published on May 1996
Locating the active sites of enzymes using mechanical properties

scientific article published on 01 May 2007
Theoretical studies of the selective binding to DNA of two non-intercalating ligands: netropsin and SN 18071

scientific article published on December 20, 1983
Investigating the local flexibility of functional residues in hemoproteins.

scientific article published on 20 January 2006
Myosin flexibility: structural domains and collective vibrations.

scientific article published in February 2004
Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA

scientific article
Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA

scientific article published on 11 May 2012
Deforming DNA: from physics to biology.

scientific article published on July 2009
Identification of protein interaction partners and protein-protein interaction sites

scientific article published on 7 August 2008
Recognizing DNA

scientific article published on 01 November 2005
Dynamics and stability of E-cadherin dimers.

scientific article published on 15 September 2006
Protein-DNA recognition triggered by a DNA conformational switch

scientific article published on 30 May 2011
Probing protein mechanics: residue-level properties and their use in defining domains.

scientific article published on September 2004
A possible family of B-like triple helix structures: comparison with the Arnott A-like triple helix

scientific article published in March 1993
Towards a molecular view of transcriptional control.

scientific article published on 30 January 2012
Modelling DNA conformational mechanics

scientific article published on 01 May 1994
Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.

scientific article published in July 2009
Arbitrary protein-protein docking targets biologically relevant interfaces.

scientific article
Probing the Flexibility of the Bacterial Reaction Center: The Wild-Type Protein Is More Rigid Than Two Site-Specific Mutants

scientific article published on 04 December 2007
The fine structure of two DNA dodecamers containing the cAMP responsive element sequence and its inverse. Nuclear magnetic resonance and molecular simulation studies.

scientific article published in October 1992
Modelling DNA stretching for physics and biology

scientific article published on 01 January 1999
Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study

scientific article published on 01 March 1994
Unusual DNA conformations.

scientific article published on June 1997
A new theoretical index of biochemical reactivity combining steric and electrostatic factors. An application to yeast tRNAPhe

scientific article published on 01 March 1984
Sequence-targeted cleavage of nucleic acids by oligo-alpha-thymidylate-phenanthroline conjugates: parallel and antiparallel double helices are formed with DNA and RNA, respectively.

scientific article
PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties.

scientific article
Docking macromolecules with flexible segments.

scientific article
The solvation contribution to the binding energy of DNA with non-intercalating antibiotics.

scientific article

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