Biological vs. Crystallographic Protein Interfaces: An Overview of Computational Approaches for Their Classification by Katarina Elez, Alexandre M. J. J. Bonvin, Anna Vangone

Get full text

Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit by Gydo C.P.van Zundert, Alexandre M.J.J. Bonvin

Get full text

ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information by Marco Giulini, Rodrigo V. Honorato, Jesús L. Rivera, Alexandre M. J. J. Bonvin

Get full text

MARTINI-Based Protein-DNA Coarse-Grained HADDOCKing by Rodrigo V. Honorato, Rodrigo V. Honorato, Jorge Roel-Touris, Alexandre M. J. J. Bonvin

Get full text

MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein–Protein Docking Conformations by Yong Jung, Cunliang Geng, Alexandre M. J. J. Bonvin, Li C. Xue, Vasant G. Honavar

Get full text

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

Get full text

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

Get full text

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

Get full text

A comprehensive framework of E2–RING E3 interactions of the human ubiquitin–proteasome system by Sjoerd J L van Wijk, Sjoerd J de Vries, Patrick Kemmeren, Anding Huang, Rolf Boelens, Alexandre M J J Bonvin, H Th Marc Timmers

Get full text

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

Get full text

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) [version 1; peer review: 1 approved, 3 approved with reservations] by Christine Orengo, Sameer Velankar, Shoshana Wodak, Vincent Zoete, Alexandre M.J.J. Bonvin, Arne Elofsson, K. Anton Feenstra, Dietland L. Gerloff, Thomas Hamelryck, John M. Hancock, Manuela Helmer-Citterich, Adam Hospital, Modesto Orozco, Anastassis Perrakis, Matthias Rarey, Claudio Soares, Joel L. Sussman, Janet M. Thornton, Pierre Tuffery, Gabor Tusnady, Rikkert Wierenga, Tiina Salminen, Bohdan Schneider

Get full text

PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation by Maria Stahl Madsen, Marjoleine F. Broekema, Martin Rønn Madsen, Arjen Koppen, Anouska Borgman, Cathrin Gräwe, Elisabeth G. K. Thomsen, Denise Westland, Mariette E. G. Kranendonk, Marian Groot Koerkamp, Nicole Hamers, Alexandre M. J. J. Bonvin, José M. Ramos Pittol, Kedar Nath Natarajan, Sander Kersten, Frank C. P. Holstege, Houshang Monajemi, Saskia W. C. van Mil, Michiel Vermeulen, Birthe B. Kragelund, David Cassiman, Susanne Mandrup, Eric Kalkhoven

Get full text