List of works - Rebecca Wade

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

scientific article published on September 2006

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

scientific article published on 01 December 2010

Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs

scientific article

The impact of protein flexibility on protein-protein docking

scientific article published on 01 January 2005

DSMM: a Database of Simulated Molecular Motions

scientific article published on January 2003

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

scientific article published on 01 June 1989

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

article

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

scientific article published on 01 July 1999

Homology modeling of the Abl-SH3 domain.

scientific article

Structural and electrostatic properties of ubiquitination and related pathways

scientific article published on May 2007

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

scientific article

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing

scientific article published on 25 September 2018

In search of the prototype of nitric oxide synthase

scientific article published in November 2003

Proteinâ surface interactions: challenging experiments and computations

scientific article published on 01 May 2010

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 published on 01 June 1992

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

scientific article published in March 2008

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

article

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

article

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

scientific article

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

scientific article published on 7 September 2009

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

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

scientific article published on 01 July 2007

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

scientific article published on September 2003

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

article

ProSAT: functional annotation of protein 3D structures

scientific article

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

scientific article published on 11 July 2016

LigDig: a web server for querying ligand-protein interactions

scientific article

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

scientific article (publication date: 2013)

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

scientific article published on 7 June 2016

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

scientific article published on May 2004

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

scientific article

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

scientific article published on April 21, 2011

Calculating enzyme kinetic parameters from protein structures

scientific article published on February 2008

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

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

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

scientific article published on 8 March 2017

Conservation and Role of Electrostatics in Thymidylate Synthase

scientific article

Using 3D protein structures to derive 3D-QSARs

scientific article published on 01 December 2004

Druggability Assessment in TRAPP Using Machine Learning Approaches

scientific article published on 11 March 2020

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

scientific article

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

scientific article

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

scientific article published on 22 October 2015

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

scientific article published on 04 October 2018

Translational repression of thymidylate synthase by targeting its mRNA.

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

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

webSDA: a web server to simulate macromolecular diffusional association

scientific article published on 16 April 2015

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

scientific article published on 15 November 2017

Halogen-Aromatic π Interactions Modulate Inhibitor Residence Times.

scientific article

ProSAT+: visualizing sequence annotations on 3D structure

scientific article

List of works by Rebecca Wade

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

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

Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs

The impact of protein flexibility on protein-protein docking

DSMM: a Database of Simulated Molecular Motions

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

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

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

Homology modeling of the Abl-SH3 domain.

Structural and electrostatic properties of ubiquitination and related pathways

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

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing

In search of the prototype of nitric oxide synthase

Proteinâ surface interactions: challenging experiments and computations

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

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

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

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

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

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

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.

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

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

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

ProSAT: functional annotation of protein 3D structures

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

LigDig: a web server for querying ligand-protein interactions

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

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

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

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

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

Calculating enzyme kinetic parameters from protein structures

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

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

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

Conservation and Role of Electrostatics in Thymidylate Synthase

Using 3D protein structures to derive 3D-QSARs

Druggability Assessment in TRAPP Using Machine Learning Approaches

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

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

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

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

Translational repression of thymidylate synthase by targeting its mRNA.

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

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

webSDA: a web server to simulate macromolecular diffusional association

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

Halogen-Aromatic π Interactions Modulate Inhibitor Residence Times.

ProSAT+: visualizing sequence annotations on 3D structure