List of works - Rebecca Wade

Simulation of the diffusional association of barnase and barstar.

scientific article published on May 1997

The ins and outs of cytochrome P450s

scientific article

How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms.

scientific article

Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations

article

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation

scientific article

Biomolecular diffusional association

scientific article

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

scientific article

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure

scientific article published on 01 May 1989

Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations

scientific article published on May 26, 1998

Brownian Dynamics Simulation of Protein–Protein Diffusional Encounter

scientific article published on March 1, 1998

Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine

scientific article

Prediction of drug binding affinities by comparative binding energy analysis

scientific article published in July 1995

Comparative kinetic analysis of FLP and cre recombinases: mathematical models for DNA binding and recombination.

scientific article published in November 1998

Diffusional encounter of barnase and barstar

scientific article published on 16 December 2005

A survey of active site access channels in cytochromes P450.

scientific article published in July 2004

Structure and dynamics of the membrane-bound cytochrome P450 2C9

scientific article

Computational approaches to identifying and characterizing protein binding sites for ligand design

scientific article published in March 2010

A tightly regulated molecular toggle controls AAA+ disaggregase

scientific article published on 18 November 2012

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?

scientific article

How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways

scientific article

Visualization of macromolecular structures

scientific article

webPIPSA: a web server for the comparison of protein interaction properties

scientific article published on 17 April 2008

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds

article

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds

article

Electrostatic Analysis and Brownian Dynamics Simulation of the Association of Plastocyanin and Cytochrome F

scientific article published on December 1, 2001

How optimal are the binding energetics of barnase and barstar?

scientific article published on September 2004

Importance of explicit salt ions for protein stability in molecular dynamics simulation.

scientific article published on 01 June 1998

Simulation of enzyme–substrate encounter with gated active sites

scientific article published on 01 January 1994

Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations.

scientific article

A mechanistic model of the cysteine synthase complex.

scientific article

Exceptionally stable salt bridges in cytochrome P450cam have functional roles.

scientific article

Protein Binding Pocket Dynamics

scientific article published on 25 April 2016

Brownian dynamics simulation of protein solutions: structural and dynamical properties

scientific article published on December 2010

Kinetics for Drug Discovery: an industry-driven effort to target drug residence time

scientific article

Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

scientific article

Docking of Ubiquitin to Gold Nanoparticles

scientific article published on 10 October 2012

Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family

scientific article published on 01 September 2004

Heterodimer formation of wild-type and amyotrophic lateral sclerosis-causing mutant Cu/Zn-superoxide dismutase induces toxicity independent of protein aggregation

scientific article published on 22 January 2008

Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes.

scientific article published in March 2001

A unique profilin-actin interface is important for malaria parasite motility

scientific article

Conformational diversity and ligand tunnels of mammalian cytochrome P450s

scientific article published on January 2013

Global profiling of SRP interaction with nascent polypeptides.

scientific article published on 3 August 2016

Structure and function of the hetero-oligomeric cysteine synthase complex in plants

scientific article published on 18 August 2010

Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding.

scientific article published on 16 June 2013

Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions

scientific article published on May 30, 2012

Improved Binding of Cytochrome P450cam Substrate Analogues Designed To Fill Extra Space in the Substrate Binding Pocket†

article

Comparative structural and energetic analysis of WW domain-peptide interactions

scientific article

Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation

article

Receptor binding properties of four-helix-bundle growth factors deduced from electrostatic analysis.

scientific article published on June 1994

List of works by Rebecca Wade

Simulation of the diffusional association of barnase and barstar.

The ins and outs of cytochrome P450s

How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms.

Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation

Biomolecular diffusional association

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure

Electrostatic steering and ionic tethering in enzyme–ligand binding: Insights from simulations

Brownian Dynamics Simulation of Protein–Protein Diffusional Encounter

Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a novel functional role for a buried arginine

Prediction of drug binding affinities by comparative binding energy analysis

Comparative kinetic analysis of FLP and cre recombinases: mathematical models for DNA binding and recombination.

Diffusional encounter of barnase and barstar

A survey of active site access channels in cytochromes P450.

Structure and dynamics of the membrane-bound cytochrome P450 2C9

Computational approaches to identifying and characterizing protein binding sites for ligand design

A tightly regulated molecular toggle controls AAA+ disaggregase

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?

How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways

Visualization of macromolecular structures

webPIPSA: a web server for the comparison of protein interaction properties

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds

Electrostatic Analysis and Brownian Dynamics Simulation of the Association of Plastocyanin and Cytochrome F

How optimal are the binding energetics of barnase and barstar?

Importance of explicit salt ions for protein stability in molecular dynamics simulation.

Simulation of enzyme–substrate encounter with gated active sites

Pathways and mechanisms for product release in the engineered haloalkane dehalogenases explored using classical and random acceleration molecular dynamics simulations.

A mechanistic model of the cysteine synthase complex.

Exceptionally stable salt bridges in cytochrome P450cam have functional roles.

Protein Binding Pocket Dynamics

Brownian dynamics simulation of protein solutions: structural and dynamical properties

Kinetics for Drug Discovery: an industry-driven effort to target drug residence time

Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

Docking of Ubiquitin to Gold Nanoparticles

Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family

Heterodimer formation of wild-type and amyotrophic lateral sclerosis-causing mutant Cu/Zn-superoxide dismutase induces toxicity independent of protein aggregation

Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes.

A unique profilin-actin interface is important for malaria parasite motility

Conformational diversity and ligand tunnels of mammalian cytochrome P450s

Global profiling of SRP interaction with nascent polypeptides.

Structure and function of the hetero-oligomeric cysteine synthase complex in plants

Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding.

Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions

Improved Binding of Cytochrome P450cam Substrate Analogues Designed To Fill Extra Space in the Substrate Binding Pocket†

Comparative structural and energetic analysis of WW domain-peptide interactions

Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation

Receptor binding properties of four-helix-bundle growth factors deduced from electrostatic analysis.