List of works - Rebecca Wade

Biochemical network-based drug-target prediction

scientific article published on 14 June 2010

A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins.

scientific article published in July 1991

On the structure and dynamics of the complex of the nucleosome and the linker histone

scientific article published on 25 February 2011

The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity

scientific article

qPIPSA: relating enzymatic kinetic parameters and interaction fields

scientific article

‘Flu’ and structure-based drug design

scientific article published on September 15, 1997

Comparative Binding Energy (COMBINE) Analysis of OppA−Peptide Complexes to Relate Structure to Binding Thermodynamics

article

Bridging from molecular simulation to biochemical networks

scientific article

The shape of protein crowders is a major determinant of protein diffusion

scientific article published on April 2013

MolSurfer: A macromolecular interface navigator

scientific article

On the Contributions of Diffusion and Thermal Activation to Electron Transfer betweenPhormidium laminosumPlastocyanin and Cytochromef: Brownian Dynamics Simulations with Explicit Modeling of Nonpolar Desolvation Interactions and Electron Transfer Eve

article

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding.

scientific article published on 22 December 2017

Multiple molecular recognition mechanisms. Cytochrome P450--a case study

scientific article

TRAPP: a tool for analysis of transient binding pockets in proteins

scientific article published on 16 May 2013

Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.

scientific article

Modeling and simulation of protein-surface interactions: achievements and challenges

scientific article published on January 2016

Novel approaches for targeting thymidylate synthase to overcome the resistance and toxicity of anticancer drugs.

scientific article published on September 2010

Homodimeric enzymes as drug targets.

scientific article published on January 2010

The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration

scientific article published on 7 March 2016

Mechanism of auxin interaction with Auxin Binding Protein (ABP1): a molecular dynamics simulation study

scientific article

Structural changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-camphor and (1S)-camphor.

scientific article published on 01 November 1996

Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis

scientific article published in May 2000

Rational modification of human synovial fluid phospholipase A2 inhibitors

article

A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB.

scientific article published on 28 June 2012

Multiple, Ligand-dependent Routes from the Active Site of Cytochrome P450 2C9

scientific article published on 01 February 2012

Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.

scientific article published in July 2001

Diffusion and association processes in biological systems: theory, computation and experiment

scientific article

GTP regulates the microtubule nucleation activity of γ-tubulin

scientific article published on 27 October 2013

Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors.

scientific article published on March 1997

Virtual screening identification of nonfolate compounds, including a CNS drug, as antiparasitic agents inhibiting pteridine reductase

scientific article

SYCAMORE--a systems biology computational analysis and modeling research environment

scientific article

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

scientific article published on 29 June 2015

Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex

scientific article

Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking

scientific article published in March 2006

Specific and non-specific effects of potassium cations on substrate-protein interactions in cytochromes P450cam and P450lin

scientific article published in September 2002

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

scientific article published on 04 June 2018

Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria

scientific article published on 17 May 2013

Analytically defined surfaces to analyze molecular interaction properties

scientific article published in December 1996

Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes.

scientific article

Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design.

scientific article

Kar1 binding to Sfi1 C-terminal regions anchors the SPB bridge to the nuclear envelope

scientific article published on 15 June 2015

ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent

scientific article published on 16 April 2010

Protein-protein docking by simulating the process of association subject to biochemical constraints

scientific article published in June 2008

Comparative binding energy analysis for binding affinity and target selectivity prediction

scientific article published in January 2010

Solvation of the active site of cytochrome P450-cam

scientific article published on 01 June 1990

Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase.

scientific article published on April 2015

Inhibitor specificity via protein dynamics: insights from the design of antibacterial agents targeted against thymidylate synthase

scientific article

Dynamics of CYP51: implications for function and inhibitor design

scientific article

Force Field Effects on a β-Sheet Protein Domain Structure in Thermal Unfolding Simulations

scientific article published in January 2006

Structural basis for the varying propensities of different amino acids to adopt the collagen conformation.

scientific article published in March 2011

List of works by Rebecca Wade

Biochemical network-based drug-target prediction

A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins.

On the structure and dynamics of the complex of the nucleosome and the linker histone

The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity

qPIPSA: relating enzymatic kinetic parameters and interaction fields

‘Flu’ and structure-based drug design

Comparative Binding Energy (COMBINE) Analysis of OppA−Peptide Complexes to Relate Structure to Binding Thermodynamics

Bridging from molecular simulation to biochemical networks

The shape of protein crowders is a major determinant of protein diffusion

MolSurfer: A macromolecular interface navigator

On the Contributions of Diffusion and Thermal Activation to Electron Transfer betweenPhormidium laminosumPlastocyanin and Cytochromef: Brownian Dynamics Simulations with Explicit Modeling of Nonpolar Desolvation Interactions and Electron Transfer Eve

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding.

Multiple molecular recognition mechanisms. Cytochrome P450--a case study

TRAPP: a tool for analysis of transient binding pockets in proteins

Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.

Modeling and simulation of protein-surface interactions: achievements and challenges

Novel approaches for targeting thymidylate synthase to overcome the resistance and toxicity of anticancer drugs.

Homodimeric enzymes as drug targets.

The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration

Mechanism of auxin interaction with Auxin Binding Protein (ABP1): a molecular dynamics simulation study

Structural changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-camphor and (1S)-camphor.

Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis

Rational modification of human synovial fluid phospholipase A2 inhibitors

A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB.

Multiple, Ligand-dependent Routes from the Active Site of Cytochrome P450 2C9

Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10.

Diffusion and association processes in biological systems: theory, computation and experiment

GTP regulates the microtubule nucleation activity of γ-tubulin

Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors.

Virtual screening identification of nonfolate compounds, including a CNS drug, as antiparasitic agents inhibiting pteridine reductase

SYCAMORE--a systems biology computational analysis and modeling research environment

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex

Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking

Specific and non-specific effects of potassium cations on substrate-protein interactions in cytochromes P450cam and P450lin

Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations

Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria

Analytically defined surfaces to analyze molecular interaction properties

Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes.

Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design.

Kar1 binding to Sfi1 C-terminal regions anchors the SPB bridge to the nuclear envelope

ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent

Protein-protein docking by simulating the process of association subject to biochemical constraints

Comparative binding energy analysis for binding affinity and target selectivity prediction

Solvation of the active site of cytochrome P450-cam

Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase.

Inhibitor specificity via protein dynamics: insights from the design of antibacterial agents targeted against thymidylate synthase

Dynamics of CYP51: implications for function and inhibitor design

Force Field Effects on a β-Sheet Protein Domain Structure in Thermal Unfolding Simulations

Structural basis for the varying propensities of different amino acids to adopt the collagen conformation.