List of works - David W. Ritchie

A structure-based classification and analysis of protein domain family binding sites and their interactions.

scientific article published on 9 April 2015

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions

scientific article published on 30 June 2008

Blind prediction of interfacial water positions in CAPRI

scientific article

Classification and Exploration of 3D Protein Domain Interactions Using Kbdock

scientific article

Clustering and classifying diverse HIV entry inhibitors using a novel consensus shape-based virtual screening approach: further evidence for multiple binding sites within the CCR5 extracellular pocket.

scientific article published in November 2008

Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking

scientific article

Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods.

scientific article

Detecting drug promiscuity using Gaussian ensemble screening

scientific article published on 19 July 2012

Discovery of novel HIV entry inhibitors for the CXCR4 receptor by prospective virtual screening.

scientific article

DockTrina: docking triangular protein trimers.

scientific article

Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2.

scientific article

Exploring c-Met kinase flexibility by sampling and clustering its conformational space.

scientific article published on 24 January 2012

Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity ⬇️

scientific article published on October 23, 2012

Flexible protein docking refinement using pose-dependent normal mode analysis.

scientific article published on 18 June 2012

GES polypharmacology fingerprints: a novel approach for drug repositioning

scientific article published on 17 February 2014

GESSE: Predicting Drug Side Effects from Drug-Target Relationships.

scientific article published on 7 August 2015

HexServer: an FFT-based protein docking server powered by graphics processors.

scientific article

Identification and characterisation of a novel immune-type receptor (NITR) gene cluster in the European sea bass, Dicentrarchus labrax, reveals recurrent gene expansion and diversification by positive selection

scientific article

Identifying and characterizing promiscuous targets: implications for virtual screening.

scientific article

KBDOCK 2013: a spatial classification of 3D protein domain family interactions.

scientific article

Modeling the structural basis of human CCR5 chemokine receptor function: from homology model building and molecular dynamics validation to agonist and antagonist docking

scientific article published on 01 May 2006

Predicting drug polypharmacology using a novel surface property similarity-based approach.

scientific article published on 19 April 2011

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

scientific article

Protein docking using case-based reasoning

scientific article published in December 2013

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. ⬇️

scientific article published on 13 July 2016

Recent Progress and Future Directions in Protein-Protein Docking

scientific article

Recent Trends and Applications in 3D Virtual Screening ⬇️

scientific article published on November 1, 2012

Recent trends and future prospects in computational GPCR drug discovery: from virtual screening to polypharmacology.

scientific article published on January 2013

Representing and comparing protein folds and fold families using three-dimensional shape-density representations.

scientific article

Spatial clustering of protein binding sites for template based protein docking

scientific article published on 27 August 2011

Toward high throughput 3D virtual screening using spherical harmonic surface representations

scientific article published on 7 September 2007

Ultra-fast FFT protein docking on graphics processors

scientific article

Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex

scientific article

Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening ⬇️

scientific article published on 04 June 2011

Using Spherical Harmonic Surface Property Representations for Ligand-Based Virtual Screening

scientific article published on 22 December 2010

gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration

scientific article published on 21 September 2013

gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy.

scientific article

List of works by David W. Ritchie

A structure-based classification and analysis of protein domain family binding sites and their interactions.

Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions

Blind prediction of interfacial water positions in CAPRI

Classification and Exploration of 3D Protein Domain Interactions Using Kbdock

Clustering and classifying diverse HIV entry inhibitors using a novel consensus shape-based virtual screening approach: further evidence for multiple binding sites within the CCR5 extracellular pocket.

Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking

Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods.

Detecting drug promiscuity using Gaussian ensemble screening

Discovery of novel HIV entry inhibitors for the CXCR4 receptor by prospective virtual screening.

DockTrina: docking triangular protein trimers.

Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2.

Exploring c-Met kinase flexibility by sampling and clustering its conformational space.

Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity ⬇️

Flexible protein docking refinement using pose-dependent normal mode analysis.

GES polypharmacology fingerprints: a novel approach for drug repositioning

GESSE: Predicting Drug Side Effects from Drug-Target Relationships.

HexServer: an FFT-based protein docking server powered by graphics processors.

Identification and characterisation of a novel immune-type receptor (NITR) gene cluster in the European sea bass, Dicentrarchus labrax, reveals recurrent gene expansion and diversification by positive selection

Identifying and characterizing promiscuous targets: implications for virtual screening.

KBDOCK 2013: a spatial classification of 3D protein domain family interactions.

Modeling the structural basis of human CCR5 chemokine receptor function: from homology model building and molecular dynamics validation to agonist and antagonist docking

Predicting drug polypharmacology using a novel surface property similarity-based approach.

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

Protein docking using case-based reasoning

Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds. ⬇️

Recent Progress and Future Directions in Protein-Protein Docking

Recent Trends and Applications in 3D Virtual Screening ⬇️

Recent trends and future prospects in computational GPCR drug discovery: from virtual screening to polypharmacology.

Representing and comparing protein folds and fold families using three-dimensional shape-density representations.

Spatial clustering of protein binding sites for template based protein docking

Toward high throughput 3D virtual screening using spherical harmonic surface representations

Ultra-fast FFT protein docking on graphics processors

Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex

Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening ⬇️

Using Spherical Harmonic Surface Property Representations for Ligand-Based Virtual Screening

gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration

gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy.