Publications by authors named "David W Ritchie"

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PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions.
Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W Ritchie, Marie-Dominique Devignes

PLoS Comput Biol· August 2021

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Using restraints in EROS-DOCK improves model quality in pairwise and multicomponent protein docking.
Maria Elisa Ruiz Echartea, David W Ritchie, Isaure Chauvot de Beauchêne

Proteins· August 2020

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GrAPFI: predicting enzymatic function of proteins from domain similarity graphs.
Bishnu Sarker, David W Ritchie, Sabeur Aridhi

BMC Bioinformatics· April 2020

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EROS-DOCK: protein-protein docking using exhaustive branch-and-bound rotational search.
Maria Elisa Ruiz Echartea, Isaure Chauvot de Beauchêne, David W Ritchie

Bioinformatics· December 2019

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Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.
Marc F Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphaël A G Chaleil, David W Ritchie

Proteins· December 2019

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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
Naihui Zhou, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee, Balint Z Kacsoh, David W Ritchie

Genome Biol· November 2019

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Characterization of a relaxase belonging to the MOB family, a widespread family in Firmicutes mediating the transfer of ICEs.
Nicolas Soler, Emilie Robert, Isaure Chauvot de Beauchêne, Philippe Monteiro, Virginie Libante, David W Ritchie

Mob DNA· May 2019

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Computational discovery of direct associations between GO terms and protein domains.
Seyed Ziaeddin Alborzi, David W Ritchie, Marie-Dominique Devignes

BMC Bioinformatics· November 2018

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PDB-wide identification of biological assemblies from conserved quaternary structure geometry.
Sucharita Dey, David W Ritchie, Emmanuel D Levy

Nat Methods· January 2018

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Classification and Exploration of 3D Protein Domain Interactions Using Kbdock.
Anisah W Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W Ritchie

Methods Mol Biol· December 2017

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Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models.
Marwa El Houasli, Bernard Maigret, Marie-Dominique Devignes, Anisah W Ghoorah, Sergei Grudinin, David W Ritchie

Proteins· March 2017

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ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains.
Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, David W Ritchie

BMC Bioinformatics· February 2017

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Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Marc F Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen-You Huang, Dina Schneidman-Duhovny, David W Ritchie

Proteins· September 2016

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Calculating and scoring high quality multiple flexible protein structure alignments.
David W Ritchie

Bioinformatics· September 2016

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PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation.
Emilie Neveu, David W Ritchie, Petr Popov, Sergei Grudinin

Bioinformatics· September 2016

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Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds.
Dzmitry Padhorny, Andrey Kazennov, Brandon S Zerbe, Kathryn A Porter, Bing Xia, David W Ritchie

Proc Natl Acad Sci U S A· July 2016

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GESSE: Predicting Drug Side Effects from Drug-Target Relationships.
Violeta I Pérez-Nueno, Michel Souchet, Arnaud S Karaboga, David W Ritchie

J Chem Inf Model· September 2015

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Unraveling the molecular architecture of a G protein-coupled receptor/β-arrestin/Erk module complex.
Thomas Bourquard, Flavie Landomiel, Eric Reiter, Pascale Crépieux, David W Ritchie

Sci Rep· June 2015

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A structure-based classification and analysis of protein domain family binding sites and their interactions.
Anisah W Ghoorah, Marie-Dominique Devignes, Seyed Ziaeddin Alborzi, Malika Smaïl-Tabbone, David W Ritchie

Biology (Basel)· April 2015

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Blind prediction of interfacial water positions in CAPRI.
Marc F Lensink, Iain H Moal, Paul A Bates, Panagiotis L Kastritis, Adrien S J Melquiond, David W Ritchie

Proteins· April 2014

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GES polypharmacology fingerprints: a novel approach for drug repositioning.
Violeta I Pérez-Nueno, Arnaud S Karaboga, Michel Souchet, David W Ritchie

J Chem Inf Model· March 2014

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KBDOCK 2013: a spatial classification of 3D protein domain family interactions.
Anisah W Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W Ritchie

Nucleic Acids Res· January 2014

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Protein docking using case-based reasoning.
Anisah W Ghoorah, Marie-Dominique Devignes, Malika Smaïl-Tabbone, David W Ritchie

Proteins· December 2013

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gEMfitter: a highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration.
Thai V Hoang, Xavier Cavin, David W Ritchie

J Struct Biol· November 2013

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gEMpicker: a highly parallel GPU-accelerated particle picking tool for cryo-electron microscopy.
Thai V Hoang, Xavier Cavin, Patrick Schultz, David W Ritchie

BMC Struct Biol· October 2013

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