Works by Bonvin, Alexandre M. J. J.

Results: 102

Towards the accurate modelling of antibody−antigen complexes from sequence using machine learning and information-driven docking.

Published in:

Bioinformatics, 2024, v. 40, n. 10, p. 1, doi. 10.1093/bioinformatics/btae583

By:

Giulini, Marco;
Schneider, Constantin;
Cutting, Daniel;
Desai, Nikita;
Deane, Charlotte M;
Bonvin, Alexandre M J J

Publication type:

Article

DeepRank-GNN: a graph neural network framework to learn patterns in protein–protein interfaces.

Published in:

Bioinformatics, 2023, v. 39, n. 1, p. 1, doi. 10.1093/bioinformatics/btac759

By:

Réau, Manon;
Renaud, Nicolas;
Xue, Li C;
Bonvin, Alexandre M J J

Publication type:

Article

proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking.

Published in:

Bioinformatics, 2020, v. 36, n. 20, p. 5107, doi. 10.1093/bioinformatics/btaa644

By:

Ambrosetti, Francesco;
Olsen, Tobias Hegelund;
Olimpieri, Pier Paolo;
Jiménez-García, Brian;
Milanetti, Edoardo;
Marcatilli, Paolo;
Bonvin, Alexandre M J J

Publication type:

Article

A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance.

Published in:

Life Science Alliance, 2023, v. 6, n. 11, p. 1, doi. 10.26508/lsa.202302058

By:

van der Krift, Felix;
Zijlmans, Dick W.;
Shukla, Rhythm;
Javed, Ali;
Koukos, Panagiotis I.;
Schwarz, Laura L. E.;
Timmermans-Sprang, Elpetra P. M.;
Maas, Peter E. M.;
Gahtory, Digvijay;
van den Nieuwboer, Maurits;
Mol, Jan A.;
Strous, Ger J.;
Bonvin, Alexandre M. J. J.;
van der Stelt, Mario;
Veldhuizen, Edwin J. A.;
Weingarth, Markus;
Vermeulen, Michiel;
Klumperman, Judith;
Maurice, Madelon M.

Publication type:

Article

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

Published in:

Crystals (2073-4352), 2020, v. 10, n. 2, p. 114, doi. 10.3390/cryst10020114

By:

Elez, Katarina;
Bonvin, Alexandre M. J. J.;
Vangone, Anna

Publication type:

Article

Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 17, p. 5634, doi. 10.1093/nar/gkq222

By:

van Dijk, Marc;
Bonvin, Alexandre M. J. J.

Publication type:

Article

3D-DART: a DNA structure modelling server.

Published in:

Nucleic Acids Research, 2009, v. 37, n. suppl_2, p. W235, doi. 10.1093/nar/gkp287

By:

van Dijk, Marc;
Bonvin, Alexandre M. J. J.

Publication type:

Article

A protein–DNA docking benchmark.

Published in:

Nucleic Acids Research, 2008, v. 36, n. 14, p. e88, doi. 10.1093/nar/gkn386

By:

van Dijk, Marc;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility.

Published in:

Nucleic Acids Research, 2006, v. 34, n. 11, p. 3317, doi. 10.1093/nar/gkl412

By:

van Dijk, Marc;
van Dijk, Aalt D. J.;
Hsu, Victor;
Boelens, Rolf;
Bonvin, Alexandre M. J. J.

Publication type:

Article

DeepRank: a deep learning framework for data mining 3D protein-protein interfaces.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-27396-0

By:

Renaud, Nicolas;
Geng, Cunliang;
Georgievska, Sonja;
Ambrosetti, Francesco;
Ridder, Lars;
Marzella, Dario F.;
Réau, Manon F.;
Bonvin, Alexandre M. J. J.;
Xue, Li C.

Publication type:

Article

Using machine‐learning‐driven approaches to boost hot‐spot's knowledge.

Published in:

WIREs: Computational Molecular Science, 2022, v. 12, n. 5, p. 1, doi. 10.1002/wcms.1602

By:

Rosário‐Ferreira, Nícia;
Bonvin, Alexandre M. J. J.;
Moreira, Irina S.

Publication type:

Article

Finding the ΔΔG spot: Are predictors of binding affinity changes upon mutations in protein–protein interactions ready for it?

Published in:

WIREs: Computational Molecular Science, 2019, v. 9, n. 5, p. N.PAG, doi. 10.1002/wcms.1410

By:

Geng, Cunliang;
Xue, Li C.;
Roel‐Touris, Jorge;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Refinement of protein structures in explicit solvent.

Published in:

Proteins, 2003, v. 50, n. 3, p. 496, doi. 10.1002/prot.10299

By:

Linge, Jens P.;
Williams, Mark A.;
Spronk, Christian A.E.M.;
Bonvin, Alexandre M. J. J.;
Nilges, Michael

Publication type:

Article

'Ensemble' iterative relaxation matrix approach: A new NMR refinement protocol applied to the solution structure of crambin.

Published in:

Proteins, 1993, v. 15, n. 4, p. 385, doi. 10.1002/prot.340150406

By:

Bonvin, Alexandre M. J. J.;
Rullmann, J. Antoon C.;
Lamerichs, Rolf M. J. N.;
Boelens, Rolf;
Kaptein, Robert

Publication type:

Article

Integrative computational modeling of protein interactions.

Published in:

FEBS Journal, 2014, v. 281, n. 8, p. 1988, doi. 10.1111/febs.12771

By:

Rodrigues, João P. G. L. M.;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Data-driven homology modelling of P-glycoprotein in the ATP-bound state indicates flexibility of the transmembrane domains.

Published in:

FEBS Journal, 2009, v. 276, n. 4, p. 964, doi. 10.1111/j.1742-4658.2008.06832.x

By:

Stockner, Thomas;
de Vries, Sjoerd J.;
Bonvin, Alexandre M. J. J.;
Ecker, Gerhard F.;
Chiba, Peter

Publication type:

Article

Data-driven docking for the study of biomolecular complexes.

Published in:

FEBS Journal, 2005, v. 272, n. 2, p. 293, doi. 10.1111/j.1742-4658.2004.04473.x

By:

van Dijk, Aalt D. J.;
Boelens, Rolf;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Solvated docking: introducing water into the modelling of biomolecular complexes.

Published in:

Bioinformatics, 2006, v. 22, n. 19, p. 2340, doi. 10.1093/bioinformatics/btl395

By:

van Dijk, Aalt D. J.;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Intramolecular surface contacts contain information about protein–protein interface regions.

Published in:

Bioinformatics, 2006, v. 22, n. 17, p. 2094

By:

Alexandre M. J. J. Bonvin

Publication type:

Article

Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy.

Published in:

Magnetic Resonance, 2021, v. 2, n. 1, p. 187, doi. 10.5194/mr-2-187-2021

By:

le Paige, Ulric B.;
Sheng Qi Xiang;
Hendrix, Marco M. R. M.;
Yi Zhang;
Folkers, Gert E.;
Weingarth, Markus;
Bonvin, Alexandre M. J. J.;
Kutateladze, Tatiana G.;
Voets, Ilja K.;
Baldus, Marc;
van Ingen, Hugo

Publication type:

Article

Unveiling the Interaction of Vanadium Compounds with Human Serum Albumin by Using <sup>1</sup>H STD NMR and Computational Docking Studies.

Published in:

European Journal of Inorganic Chemistry, 2013, v. 2013, n. 26, p. 4619, doi. 10.1002/ejic.201300419

By:

Dias, David M.;
Rodrigues, João P. G. L. M.;
Domingues, Neuza S.;
Bonvin, Alexandre M. J. J.;
Castro, M. Margarida C. A.

Publication type:

Article

Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis.

Published in:

International Journal of Molecular Sciences, 2018, v. 19, n. 10, p. 2928, doi. 10.3390/ijms19102928

By:

Roseboom, Winfried;
Nazir, Madhvi G.;
Meiresonne, Nils Y.;
Mohammadi, Tamimount;
Verheul, Jolanda;
Buncherd, Hansuk;
Bonvin, Alexandre M. J. J.;
de Koning, Leo J.;
de Koster, Chris G.;
de Jong, Luitzen;
den Blaauwen, Tanneke

Publication type:

Article

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

Published in:

International Journal of Molecular Sciences, 2016, v. 17, n. 8, p. 1215, doi. 10.3390/ijms17081215

By:

Melo, Rita;
Fieldhouse, Robert;
Melo, André;
Correia, João D. G.;
Cordeiro, Maria Natália D. S.;
Gümüş, Zeynep H.;
Costa, Joaquim;
Bonvin, Alexandre M. J. J.;
Moreira, Irina S.

Publication type:

Article

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

Published in:

International Journal of Molecular Sciences, 2016, v. 17, n. 1, p. 22, doi. 10.3390/ijms17010022

By:

Kalia, Munishikha;
Willkomm, Sarah;
Claussen, Jens Christian;
Restle, Tobias;
Bonvin, Alexandre M. J. J.

Publication type:

Article

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

Published in:

BMC Bioinformatics, 2018, v. 19, n. 15, p. 19, doi. 10.1186/s12859-018-2414-9

By:

Elez, Katarina;
Bonvin, Alexandre M. J. J.;
Vangone, Anna

Publication type:

Article

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study.

Published in:

Proteomics, 2023, v. 23, n. 17, p. 1, doi. 10.1002/pmic.202200323

By:

Schweke, Hugo;
Xu, Qifang;
Tauriello, Gerardo;
Pantolini, Lorenzo;
Schwede, Torsten;
Cazals, Frédéric;
Lhéritier, Alix;
Fernandez‐Recio, Juan;
Rodríguez‐Lumbreras, Luis Angel;
Schueler‐Furman, Ora;
Varga, Julia K.;
Jiménez‐García, Brian;
Réau, Manon F.;
Bonvin, Alexandre M. J. J.;
Savojardo, Castrense;
Martelli, Pier‐Luigi;
Casadio, Rita;
Tubiana, Jérôme;
Wolfson, Haim J.;
Oliva, Romina

Publication type:

Article

Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3.

Published in:

Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 1, p. 83, doi. 10.1007/s10822-018-0148-4

By:

Koukos, Panagiotis I.;
Xue, Li C.;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Direct nuclear Overhauser effect refinement of crambin from two-dimensional nmr data using a slow-cooling annealing protocol.

Published in:

Biopolymers, 1994, v. 34, n. 1, p. 39, doi. 10.1002/bip.360340106

By:

Bonvin, Alexandre M. J. J.;
Boelens, Rolf;
Kaptein, Robert

Publication type:

Article

Computational approaches to therapeutic antibody design: established methods and emerging trends.

Published in:

Briefings in Bioinformatics, 2020, v. 21, n. 5, p. 1549, doi. 10.1093/bib/bbz095

By:

Norman, Richard A;
Ambrosetti, Francesco;
Bonvin, Alexandre M J J;
Colwell, Lucy J;
Kelm, Sebastian;
Kumar, Sandeep;
Krawczyk, Konrad

Publication type:

Article

Template-based protein-protein docking exploiting pairwise interfacial residue restraints.

Published in:

Briefings in Bioinformatics, 2017, v. 18, n. 3, p. 458, doi. 10.1093/bib/bbw027

By:

Li C. Xue;
Rodrigues, João P. G. L. M.;
Dobbs, Drena;
Honavar, Vasant;
Bonvin, Alexandre M. J. J.

Publication type:

Article

PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-34766-9

By:

Madsen, Maria Stahl;
Broekema, Marjoleine F.;
Madsen, Martin Rønn;
Koppen, Arjen;
Borgman, Anouska;
Gräwe, Cathrin;
Thomsen, Elisabeth G. K.;
Westland, Denise;
Kranendonk, Mariette E. G.;
Koerkamp, Marian Groot;
Hamers, Nicole;
Bonvin, Alexandre M. J. J.;
Pittol, José M. Ramos;
Natarajan, Kedar Nath;
Kersten, Sander;
Holstege, Frank C. P.;
Monajemi, Houshang;
van Mil, Saskia W. C.;
Vermeulen, Michiel;
Kragelund, Birthe B.

Publication type:

Article

The HADDOCK2.4 web server for integrative modeling of biomolecular complexes.

Published in:

Nature Protocols, 2024, v. 19, n. 11, p. 3219, doi. 10.1038/s41596-024-01011-0

By:

Honorato, Rodrigo V.;
Trellet, Mikael E.;
Jiménez-García, Brian;
Schaarschmidt, Jörg J.;
Giulini, Marco;
Reys, Victor;
Koukos, Panagiotis I.;
Rodrigues, João P. G. L. M.;
Karaca, Ezgi;
van Zundert, Gydo C. P.;
Roel-Touris, Jorge;
van Noort, Charlotte W.;
Jandová, Zuzana;
Melquiond, Adrien S. J.;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Defining distance restraints in HADDOCK.

Published in:

Nature Protocols, 2018, v. 13, n. 7, p. 1503, doi. 10.1038/s41596-018-0017-6

By:

Bonvin, Alexandre M. J. J.;
Karaca, Ezgi;
Kastritis, Panagiotis L.;
Rodrigues, João P. G. L. M.

Publication type:

Article

A structure-based benchmark for protein-protein binding affinity.

Published in:

Protein Science: A Publication of the Protein Society, 2011, v. 20, n. 3, p. 482, doi. 10.1002/pro.580

By:

Kastritis, Panagiotis L.;
Moal, Iain H.;
Hwang, Howook;
Weng, Zhiping;
Bates, Paul A.;
Bonvin, Alexandre M. J. J.;
Janin, Joël

Publication type:

Article

LightDock goes information-driven.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 950, doi. 10.1093/bioinformatics/btz642

By:

Roel-Touris, Jorge;
Bonvin, Alexandre M J J;
Jiménez-García, Brian

Publication type:

Article

iScore: a novel graph kernel-based function for scoring protein–protein docking models.

Published in:

Bioinformatics, 2020, v. 36, n. 1, p. 112, doi. 10.1093/bioinformatics/btz496

By:

Geng, Cunliang;
Jung, Yong;
Renaud, Nicolas;
Honavar, Vasant;
Bonvin, Alexandre M J J;
Xue, Li C

Publication type:

Article

Large-scale prediction of binding affinity in protein–small ligand complexes: the PRODIGY-LIG web server.

Published in:

Bioinformatics, 2019, v. 35, n. 9, p. 1585, doi. 10.1093/bioinformatics/bty816

By:

Vangone, Anna;
Schaarschmidt, Joerg;
Koukos, Panagiotis;
Geng, Cunliang;
Citro, Nevia;
Trellet, Mikael E;
Xue, Li C;
Bonvin, Alexandre M J J

Publication type:

Article

Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.

Published in:

Proteins, 2023, v. 91, n. 12, p. 1658, doi. 10.1002/prot.26609

By:

Lensink, Marc F.;
Brysbaert, Guillaume;
Raouraoua, Nessim;
Bates, Paul A.;
Giulini, Marco;
Honorato, Rodrigo V.;
van Noort, Charlotte;
Teixeira, Joao M. C.;
Bonvin, Alexandre M. J. J.;
Ren Kong;
Hang Shi;
Xufeng Lu;
Shan Chang;
Jian Liu;
Zhiye Guo;
Xiao Chen;
Morehead, Alex;
Roy, Raj S.;
Tianqi Wu;
Giri, Nabin

Publication type:

Article

Improving the quality of co‐evolution intermolecular contact prediction with DisVis.

Published in:

Proteins, 2023, v. 91, n. 10, p. 1407, doi. 10.1002/prot.26514

By:

van Keulen, Siri C.;
Bonvin, Alexandre M. J. J.

Publication type:

Article

PDB‐tools web: A user‐friendly interface for the manipulation of PDB files.

Published in:

Proteins, 2021, v. 89, n. 3, p. 330, doi. 10.1002/prot.26018

By:

Jiménez‐García, Brian;
Teixeira, João M. C.;
Trellet, Mikael;
Rodrigues, João P. G. L. M.;
Bonvin, Alexandre M. J. J.

Publication type:

Article

An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45.

Published in:

Proteins, 2020, v. 88, n. 8, p. 1029, doi. 10.1002/prot.25869

By:

Koukos, Panagiotis I.;
Roel‐Touris, Jorge;
Ambrosetti, Francesco;
Geng, Cunliang;
Schaarschmidt, Jörg;
Trellet, Mikael E.;
Melquiond, Adrien S. J.;
Xue, Li C.;
Honorato, Rodrigo V.;
Moreira, Irina;
Kurkcuoglu, Zeynep;
Vangone, Anna;
Bonvin, Alexandre M. J. J.

Publication type:

Article

The structural details of the interaction of single‐stranded DNA binding protein hSSB2 (NABP1/OBFC2A) with UV‐damaged DNA.

Published in:

Proteins, 2020, v. 88, n. 2, p. 319, doi. 10.1002/prot.25806

By:

Lawson, Teegan;
El‐Kamand, Serene;
Boucher, Didier;
Duong, Duc Cong;
Kariawasam, Ruvini;
Bonvin, Alexandre M. J. J.;
Richard, Derek J.;
Gamsjaeger, Roland;
Cubeddu, Liza

Publication type:

Article

Pre‐ and post‐docking sampling of conformational changes using ClustENM and HADDOCK for protein‐protein and protein‐DNA systems.

Published in:

Proteins, 2020, v. 88, n. 2, p. 292, doi. 10.1002/prot.25802

By:

Kurkcuoglu, Zeynep;
Bonvin, Alexandre M. J. J.

Publication type:

Article

iSEE: Interface structure, evolution, and energy‐based machine learning predictor of binding affinity changes upon mutations.

Published in:

Proteins, 2019, v. 87, n. 2, p. 110, doi. 10.1002/prot.25630

By:

Geng, Cunliang;
Vangone, Anna;
Folkers, Gert E.;
Xue, Li C.;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Cover Image, Volume 86, Issue S1.

Published in:

Proteins, 2018, v. 86, n. 1, p. C1, doi. 10.1002/prot.25475

By:

Schaarschmidt, Joerg;
Monastyrskyy, Bohdan;
Kryshtafovych, Andriy;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age.

Published in:

Proteins, 2018, v. 86, n. 1, p. 51, doi. 10.1002/prot.25407

By:

Schaarschmidt, Joerg;
Monastyrskyy, Bohdan;
Kryshtafovych, Andriy;
Bonvin, Alexandre M. J. J.

Publication type:

Article

A benchmark testing ground for integrating homology modeling and protein docking.

Published in:

Proteins, 2017, v. 85, n. 1, p. 10, doi. 10.1002/prot.25063

By:

Bohnuud, Tanggis;
Luo, Lingqi;
Wodak, Shoshana J.;
Bonvin, Alexandre M. J. J.;
Weng, Zhiping;
Vajda, Sandor;
Schueler‐Furman, Ora;
Kozakov, Dima

Publication type:

Article

Non-interacting surface solvation and dynamics in protein-protein interactions.

Published in:

Proteins, 2015, v. 83, n. 3, p. 445, doi. 10.1002/prot.24741

By:

Visscher, Koen M.;
Kastritis, Panagiotis L.;
Bonvin, Alexandre M. J. J.

Publication type:

Article

Blind prediction of interfacial water positions in CAPRI.

Published in:

Proteins, 2014, v. 82, n. 4, p. 620, doi. 10.1002/prot.24439

By:

Lensink, Marc F.;
Moal, Iain H.;
Bates, Paul A.;
Kastritis, Panagiotis L.;
Melquiond, Adrien S. J.;
Karaca, Ezgi;
Schmitz, Christophe;
Dijk, Marc;
Bonvin, Alexandre M. J. J.;
Eisenstein, Miriam;
Jiménez‐García, Brian;
Grosdidier, Solène;
Solernou, Albert;
Pérez‐Cano, Laura;
Pallara, Chiara;
Fernández‐Recio, Juan;
Xu, Jianqing;
Muthu, Pravin;
Praneeth Kilambi, Krishna;
Gray, Jeffrey J.

Publication type:

Article

Defining the limits of homology modeling in information-driven protein docking.

Published in:

Proteins, 2013, v. 81, n. 12, p. 2119, doi. 10.1002/prot.24382

By:

Rodrigues, J. P. G. L. M.;
Melquiond, A. S. J.;
Karaca, E.;
Trellet, M.;
Dijk, M.;
Zundert, G. C. P.;
Schmitz, C.;
Vries, S. J.;
Bordogna, A.;
Bonati, L.;
Kastritis, P. L.;
Bonvin, Alexandre M. J. J.

Publication type:

Article