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List of works by Richard Lavery

A Protein Solvation Model Based on Residue Burial.

scientific article

A free energy pathway for the interaction of the SRY protein with its binding site on DNA from atomistic simulations

scientific article published on 01 July 2009

A molecular dynamics study of adenylyl cyclase: The impact of ATP and G-protein binding.

scientific article

A new theoretical index of biochemical reactivity combining steric and electrostatic factors. An application to yeast tRNAPhe

scientific article published on 01 March 1984

A possible family of B-like triple helix structures: comparison with the Arnott A-like triple helix

scientific article published in March 1993

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

scientific article

ARTIST: an activated method in internal coordinate space for sampling protein energy landscapes

scientific article published in June 2006

Analyzing ion distributions around DNA.

scientific article

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

scientific article

Analyzing protein-DNA recognition mechanisms

scientific article published in January 2004

Arbitrary protein-protein docking targets biologically relevant interfaces.

scientific article

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

scientific article

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

scientific article

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures

scientific article

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

Conformational analysis of nucleic acids revisited: Curves+

scientific article (publication date: September 2009)

Conformational and helicoidal analysis of the molecular dynamics of proteins: "curves," dials and windows for a 50 psec dynamic trajectory of BPTI

scientific article published on 01 January 1990

Conformational sub-states in B-DNA.

scientific article published in August 1992

DNA flexibility as a function of allomorphic conformation and of base sequence

scientific article published in August 1992

DNA: an extensible molecule.

scientific article

Deforming DNA: from physics to biology.

scientific article published on July 2009

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

scientific article

Docking macromolecules with flexible segments.

scientific article

Dynamics and stability of E-cadherin dimers.

scientific article published on 15 September 2006

Exciton states of dynamic DNA double helices: alternating dCdG sequences

scientific article published on 01 August 2005

Exploring polymorphisms in B-DNA helical conformations.

scientific article published on 24 September 2012

Identification of protein interaction partners and protein-protein interaction sites

scientific article published on 7 August 2008

Improving the treatment of coarse-grain electrostatics: CVCEL

scientific article published on 01 December 2015

Intrinsic electrostatic properties and base sequence effects in the structure of oligonucleotides

scientific article published on 01 July 1982

Investigating the local flexibility of functional residues in hemoproteins.

scientific article published on 20 January 2006

Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling

scientific article

Kinking occurs during molecular dynamics simulations of small DNA minicircles

scientific article published in October 2006

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

scientific article

Locating the active sites of enzymes using mechanical properties

scientific article published on 01 May 2007

Low-frequency vibrations in alpha-helices: helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories

scientific article published in June 1995

Measuring the geometry of DNA grooves

scientific article published in March 1994

Modeling DNA deformations induced by minor groove binding proteins

scientific article published on 01 April 1999

Modeling multi-component protein-DNA complexes: the role of bending and dimerization in the complex of p53 dimers with DNA.

scientific article published on April 2001

Modeling the mechanical response of proteins to anisotropic deformation.

scientific article published in January 2009

Modelling DNA conformational mechanics

scientific article published on 01 May 1994

Modelling DNA stretching for physics and biology

scientific article published on 01 January 1999

Modelling extreme stretching of DNA.

scientific article published on June 1996

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

scientific article

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

scientific article published on May 1996

Motifs in nucleic acids: molecular mechanics restraints for base pairing and base stacking

scientific article published on 01 January 2003

Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties

scientific article published on 03 February 2020

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

scientific article published on 11 May 2012

Myosin flexibility: structural domains and collective vibrations.

scientific article published in February 2004

Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.

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

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

scientific article

Packing and recognition of protein structural elements: a new approach applied to the 4-helix bundle of myohemerythrin

scientific article published on 01 April 1993

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

scientific article published on 01 March 1993

Prediction of the positioning of the seven transmembrane alpha-helices of bacteriorhodopsin. A molecular simulation study

scientific article published on 01 March 1994

Probing protein mechanics: residue-level properties and their use in defining domains.

scientific article published on September 2004

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

Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies

scientific article published on 07 October 2009

Protein-DNA recognition triggered by a DNA conformational switch

scientific article published on 30 May 2011

Recognizing DNA

scientific article published on 01 November 2005

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

Strand orientation of [alpha]-oligodeoxynucleotides in triple helix structures: dependence on nucleotide sequence

scientific article published on September 1, 1992

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

scientific article

Temperature dependence of the DNA double helix at the nanoscale: structure, elasticity, and fluctuations.

scientific article published on October 2013

The effects of countercation screening on the electrostatic potential of DNA. The rôle of the nucleic acid conformation

scientific article published on 01 June 1982

The electrostatic field of the component units of DNA and its relationship to hydration

scientific article published on 01 January 1983

The electrostatic molecular potential of tRNAPhe. IV. The potentials and steric accessibilities of sites associated with the bases.

scientific article published on November 1980

The electrostatic potential and steric accessibility of reactive sites within Z-DNA

scientific article published on September 1980

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

The molecular electrostatic potential and steric accessibility of double-helical A-RNA.

scientific article published in July 1982

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.

scientific article

The molecular electrostatic potential and steric accessibility of poly (dI.dC). Comparison with poly (dG.dC).

scientific article

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

scientific article

Theoretical prediction of base sequence effects in DNA. Experimental reactivity of Z-DNA and B-Z transition enthalpies

scientific article published in May 1989

Theoretical studies of DNA-RNA hybrid conformations.

scientific article published on April 1994

Theoretical studies of the selective binding to DNA of two non-intercalating ligands: netropsin and SN 18071 ⬇️

scientific article published on December 20, 1983

Theoretical studies on the interaction of proteins and nucleic acid. II. The binding of alpha-helix to B-DNA

scientific article published on 01 December 1986

Towards a molecular view of transcriptional control.

scientific article published on 30 January 2012

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA

scientific article

Unusual DNA conformations.

scientific article published on June 1997

Wringing out DNA

scientific article published on 05 May 2006

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

scientific article

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