Coarse-grained (hybrid) integrative modeling of biomolecular interactions

by Jorge Roel-Touris, Alexandre M.J.J. Bonvin
Published 2020-01-01

Biological vs. Crystallographic Protein Interfaces: An Overview of Computational Approaches for Their Classification

by Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone
Published 2020-02-01

Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification

by Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone
Published 2018-11-01

CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK.

by Sjoerd J de Vries, Alexandre M J J Bonvin
Published 2011-01-01

A unified conformational selection and induced fit approach to protein-peptide docking.

by Mikael Trellet, Adrien S J Melquiond, Alexandre M J J Bonvin
Published 2013-01-01

Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit

by Gydo C.P.van Zundert, Alexandre M.J.J. Bonvin
Published 2015-04-01

Integrative modeling of membrane-associated protein assemblies

by Jorge Roel-Touris, Brian Jiménez-García, Alexandre M. J. J. Bonvin
Published 2020-12-01

Novel Insights into Guide RNA 5′-Nucleoside/Tide Binding by Human Argonaute 2

by Munishikha Kalia, Sarah Willkomm, Jens Christian Claussen, Tobias Restle, Alexandre M. J. J. Bonvin
Published 2015-12-01

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing

by Rodrigo V. Honorato, Rodrigo V. Honorato, Jorge Roel-Touris, Alexandre M. J. J. Bonvin
Published 2019-10-01

iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines

by Nicolas Renaud, Yong Jung, Vasant Honavar, Cunliang Geng, Alexandre M.J.J. Bonvin, Li C. Xue
Published 2020-01-01

Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations

by Giulia Palermo, Alexandre M. J. J. Bonvin, Matteo Dal Peraro, Rommie E. Amaro, Valentina Tozzini, Valentina Tozzini
Published 2020-08-01

pdb-tools: a swiss army knife for molecular structures [version 1; referees: 2 approved]

by João P. G. L. M. Rodrigues, João M.C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
Published 2018-12-01

Understanding the role of the Josephin domain in the PolyUb binding and cleavage properties of ataxin-3.

by Giuseppe Nicastro, Sokol V Todi, Ezgi Karaca, Alexandre M J J Bonvin, Henry L Paulson, Annalisa Pastore
Published 2010-08-01

Dynamic control of selectivity in the ubiquitination pathway revealed by an ASP to GLU substitution in an intra-molecular salt-bridge network.

by Sjoerd J L van Wijk, Adrien S J Melquiond, Sjoerd J de Vries, H Th Marc Timmers, Alexandre M J J Bonvin
Published 2012-01-01

dMM-PBSA: a new HADDOCK scoring function for protein-peptide docking

by Dimitrios Spiliotopoulos, Panagiotis L Kastritis, Panagiotis L Kastritis, Adrien Melquiond, Alexandre M.J.J. Bonvin, Giovanna Musco, Walter Rocchia, Andrea Spitaleri
Published 2016-08-01

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

by Rodrigo V. Honorato, Panagiotis I. Koukos, Brian Jiménez-García, Andrei Tsaregorodtsev, Marco Verlato, Andrea Giachetti, Antonio Rosato, Alexandre M. J. J. Bonvin
Published 2021-07-01

Antimicrobial and efflux pump inhibitory activity of caffeoylquinic acids from Artemisia absinthium against gram-positive pathogenic bacteria.

by Yiannis C Fiamegos, Panagiotis L Kastritis, Vassiliki Exarchou, Haley Han, Alexandre M J J Bonvin, Jacques Vervoort, Kim Lewis, Michael R Hamblin, George P Tegos
Published 2011-04-01

A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces

by Rita Melo, Robert Fieldhouse, André Melo, João D. G. Correia, Maria Natália D. S. Cordeiro, Zeynep H. Gümüş, Joaquim Costa, Alexandre M. J. J. Bonvin, Irina S. Moreira
Published 2016-07-01

Sequence co-evolution gives 3D contacts and structures of protein complexes

by Thomas A Hopf, Charlotta P I Schärfe, João P G L M Rodrigues, Anna G Green, Oliver Kohlbacher, Chris Sander, Alexandre M J J Bonvin, Debora S Marks
Published 2014-09-01

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots

by Irina S. Moreira, Panagiotis I. Koukos, Rita Melo, Jose G. Almeida, Antonio J. Preto, Joerg Schaarschmidt, Mikael Trellet, Zeynep H. Gümüş, Joaquim Costa, Alexandre M. J. J. Bonvin
Published 2017-08-01