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List of works by Rebecca C Wade

A Quantitative, Real-Time Assessment of Binding of Peptides and Proteins to Gold Surfaces

scientific article published on 01 December 2010

A mechanistic model of the cysteine synthase complex.

scientific article

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

scientific article published in July 1991

A multiscale approach to simulating the conformational properties of unbound multi-C₂H₂ zinc finger proteins

scientific article

A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: application to auxins

scientific article published in September 2003

A novel homozygous ARL13B variant in patients with Joubert syndrome impairs its guanine nucleotide-exchange factor activity.

scientific article published on 15 November 2017

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

A survey of active site access channels in cytochromes P450.

scientific article published in July 2004

A tightly regulated molecular toggle controls AAA+ disaggregase.

scientific article published on 18 November 2012

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

scientific article

A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories

scientific article published on 01 September 2020

Allosterically gated enzyme dynamics in the cysteine synthase complex regulate cysteine biosynthesis in Arabidopsis thaliana

scientific article

An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association

scientific article published on 27 July 2016

Analytically defined surfaces to analyze molecular interaction properties

scientific article published in December 1996

Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition

scientific article published on 7 July 2017

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

scientific article published on May 30, 2012

Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformation. I. Mapping the rotamers of residue 188 of viral protein 1.

scientific article published in June 1992

Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. II. Calculation of free-energy differences by thermodynamic integration.

scientific article

Biochemical network-based drug-target prediction

scientific article published on 14 June 2010

Biomolecular diffusional association

scientific article

Bridging from molecular simulation to biochemical networks.

scientific article

Brownian Dynamics Simulation of Protein–Protein Diffusional Encounter ⬇️

scientific article published on March 1, 1998

Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics

scientific article published on 30 March 2021

Brownian dynamics simulation of protein solutions: structural and dynamical properties

scientific article published on December 2010

COMBINE analysis of the specificity of binding of Ras proteins to their effectors

article

Calculating enzyme kinetic parameters from protein structures

scientific article published on February 2008

Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity.

scientific article published on 8 March 2017

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows

scientific article published on 06 July 2022

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

article

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

scientific article published in March 2001

Comparative binding energy analysis for binding affinity and target selectivity prediction

scientific article published in January 2010

Comparative binding energy analysis of haloalkane dehalogenase substrates: modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations.

scientific article published on May 2003

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

scientific article published in July 2001

Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties

scientific article

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

scientific article published in November 1998

Comparative mapping of on-targets and off-targets for the discovery of anti-trypanosomatid folate pathway inhibitors

scientific article published on 19 September 2017

Comparative structural and energetic analysis of WW domain-peptide interactions

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

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

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

scientific article published in March 2010

Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins.

scientific article published on May 2004

Concerted simulations reveal how peroxidase compound III formation results in cellular oscillations

scientific article published on September 2003

Conformational diversity and ligand tunnels of mammalian cytochrome P450s

scientific article published on January 2013

Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome

scientific article published on 7 June 2016

Conservation and Role of Electrostatics in Thymidylate Synthase

scientific article

Contact Map Fingerprints of Protein–Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics

scientific article published on 08 September 2021

Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields

scientific article published on 7 September 2009

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation

scientific article

DSMM: a Database of Simulated Molecular Motions

scientific article published on January 2003

Design and characterization of a mutation outside the active site of human thymidylate synthase that affects ligand binding.

scientific article published on 2 December 2009

Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family

scientific article published on 01 September 2004

Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19

scientific article published on 04 September 2019

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

scientific article

Diffusion of hydrophobin proteins in solution and interactions with a graphite surface ⬇️

scientific article published on April 21, 2011

Diffusional encounter of barnase and barstar

scientific article published on 16 December 2005

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

scientific article

Docking of Ubiquitin to Gold Nanoparticles

scientific article published on 10 October 2012

Druggability Assessment in TRAPP Using Machine Learning Approaches

scientific article published on 11 March 2020

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

scientific article published on 16 June 2013

Dynamics of CYP51: implications for function and inhibitor design

scientific article

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

scientific article published on May 26, 1998

Elusive recognition determinants for ubiquitination

scientific article

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

scientific article published on 04 June 2018

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

scientific article

Exceptionally stable salt bridges in cytochrome P450cam have functional roles.

scientific article

FTIR studies of the redox partner interaction in cytochrome P450: the Pdx-P450cam couple

scientific article published on September 2006

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

scientific article published in January 2006

Foreword Preface to the JMR Special Issue on ‘Dynamic Aspects of Molecular Recognition’

article published in 2010

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

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

G Protein-Coupled Receptor–Ligand Dissociation Rates and Mechanisms from τRAMD Simulations

scientific article published on 08 September 2021

GTP regulates the microtubule nucleation activity of γ-tubulin

scientific article published on 27 October 2013

Global profiling of SRP interaction with nascent polypeptides.

scientific article published on 3 August 2016

Halogen-Aromatic π Interactions Modulate Inhibitor Residence Times.

scientific article

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

Homodimeric enzymes as drug targets.

scientific article published on January 2010

Homology modeling of the Abl-SH3 domain.

scientific article

Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family

article

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

scientific article published on April 2015

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

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

How optimal are the binding energetics of barnase and barstar?

scientific article published on September 2004

Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen

scientific article published in June 2016

Identifying targets for bioreductive agents: Using GRID to predict selective binding regions of proteins

scientific article published on 01 June 1989

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

article

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

scientific article

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

article

In search of the prototype of nitric oxide synthase

scientific article published in November 2003

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

scientific article

KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding

scientific article published on 20 August 2019

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

scientific article published on 15 June 2015

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

scientific article

LigDig: a web server for querying ligand-protein interactions

scientific article

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

scientific article

Ligand-based discovery of N-(1,3-dioxo-1H,3H-benzo[de]isochromen-5-yl)-carboxamide and sulfonamide derivatives as thymidylate synthase A inhibitors

scientific article

Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules

scientific article

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

scientific article

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

scientific article published on January 2016

Modeling three-dimensional structure and electrostatics of alkali-stable cyclomaltodextrin glucanotransferase

article

MolSurfer: A macromolecular interface navigator

scientific article

MolSurfer: two-dimensional maps for navigating three-dimensional structures of proteins

scientific article published on 01 July 1999

Molecular Modeling in Drug Design

scientific article published on 17 January 2019

Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding.

scientific article

Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam.

scientific article

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

scientific article

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

scientific article published on 01 February 2012

Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations

scientific article published on 05 November 2021

Myotubularin-related protein 7 activates peroxisome proliferator-activated receptor-gamma

scientific article published on 10 June 2020

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

scientific article published on 01 May 1989

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

scientific article published on September 2010

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

scientific article published in May 2000

On calculation of the electrostatic potential of a phosphatidylinositol phosphate-containing phosphatidylcholine lipid membrane accounting for membrane dynamics

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

On the Use of Elevated Temperature in Simulations To Study Protein Unfolding Mechanisms

scientific article published on 01 July 2007

On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer

article

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

scientific article published on 25 February 2011

On the use of PIPSA to guide target-selective drug design

scientific article published in March 2008

Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria

scientific article (publication date: 2013)

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

scientific article

Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets

scientific article published on 11 July 2016

Prediction of Drug-Target Binding Kinetics by Comparative Binding Energy Analysis

scientific article published on 04 October 2018

Prediction of drug binding affinities by comparative binding energy analysis

scientific article published in July 1995

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

scientific article

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

scientific article published on 16 April 2010

ProSAT+: visualizing sequence annotations on 3D structure

scientific article

ProSAT: functional annotation of protein 3D structures.

scientific article

Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs

scientific article

Protein Binding Pocket Dynamics

scientific article published on 25 April 2016

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding.

scientific article published on 22 December 2017

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

article

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

scientific article published in June 2008

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

scientific article

Proteinâ surface interactions: challenging experiments and computations

scientific article published on 01 May 2010

Putative second hit rare genetic variants in families with seemingly GBA-associated Parkinson's disease

scientific article published on 05 January 2021

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

scientific article

Rational modification of human synovial fluid phospholipase A2 inhibitors

article

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

scientific article published on June 1994

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

scientific article

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

scientific article published on 30 October 2019

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

scientific article published on 17 May 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

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

scientific article published on 29 June 2015

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

scientific article

Simulation of enzyme–substrate encounter with gated active sites

scientific article published on 01 January 1994

Simulation of the diffusional association of barnase and barstar.

scientific article published on May 1997

Solvation of the active site of cytochrome P450-cam

scientific article published on 01 June 1990

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

scientific article published in September 2002

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

scientific article

Structural and electrostatic properties of ubiquitination and related pathways

scientific article published on May 2007

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

scientific article published in March 2011

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

scientific article

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

scientific article

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

scientific article published on 18 August 2010

TRAJAN: a tool for analyzing trajectories from molecular simulations

scientific article published in June 1996

TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.

scientific article

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

scientific article published on 16 May 2013

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

scientific article published on 7 March 2016

The active-inactive transition of human thymidylate synthase: Targeted molecular dynamics simulations

article

The impact of protein flexibility on protein-protein docking

scientific article published on 01 January 2005

The ins and outs of cytochrome P450s.

scientific article

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

scientific article

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

scientific article published on April 2013

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing

scientific article published on 25 September 2018

Theory and simulation: pushing the limits

Three steps to gold: mechanism of protein adsorption revealed by Brownian and molecular dynamics simulations.

scientific article

Translational repression of thymidylate synthase by targeting its mRNA.

scientific article

Using 3D protein structures to derive 3D-QSARs

scientific article published on 01 December 2004

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

scientific article

Visualization of macromolecular structures.

scientific article

When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces

scientific article published on 22 October 2015

qPIPSA: relating enzymatic kinetic parameters and interaction fields.

scientific article

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

scientific article published on 17 April 2008

webSDA: a web server to simulate macromolecular diffusional association

scientific article published on 16 April 2015

‘Flu’ and structure-based drug design ⬇️

scientific article published on September 15, 1997

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