Alexandre M J J Bonvin (A M J J Bonvin, Alexandre Mjj Bonvin)

ResearcherID Loop profile Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 55

Top Venues

Proteins

Nature communications

Communications biology

Biomolecules

This page only lists publications with an associated author ORCID identifier.

Publications

Marco Giulini, Rodrigo V Honorato, Jesús L Rivera, Alexandre M J J Bonvin
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information. Communications biology 7 (1) (2024)
Xiaotong Xu, Alexandre M J J Bonvin
DeepRank-GNN-esm: a graph neural network for scoring protein-protein models using protein language model. Bioinformatics advances 4 (1) (2024)
Andrea Basciu, Mohd Athar, Han Kurt, Christine Neville, Giuliano Malloci, Fabrizio C Muredda, Andrea Bosin, Paolo Ruggerone, Alexandre M J J Bonvin, Attilio Vittorio Vargiu
Predicting binding events in very flexible, allosteric, multi-domain proteins. bioRxiv : the preprint server for biology (2024)
Marco Giulini, Rodrigo V Honorato, Jesús L Rivera, Alexandre M J J Bonvin
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information. Communications biology 7 (1) (2024)
Rodrigo V Honorato, Mikael E Trellet, Brian Jiménez-García, Jörg J Schaarschmidt, Marco Giulini, Victor Reys, Panagiotis I Koukos, João P G L M Rodrigues, Ezgi Karaca, Gydo C P van Zundert, Jorge Roel-Touris, Charlotte W van Noort, Zuzana Jandová, Adrien S J Melquiond, Alexandre M J J Bonvin
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes. Nature protocols (2024)
Xiaotong Xu, Alexandre M J J Bonvin
DeepRank-GNN-esm: a graph neural network for scoring protein-protein models using protein language model. Bioinformatics advances 4 (1) (2024)
Marco Giulini, Rodrigo V Honorato, Jesús L Rivera, Alexandre M J J Bonvin
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information. Communications biology 7 (1) (2024)
Andrea Basciu, Mohd Athar, Han Kurt, Christine Neville, Giuliano Malloci, Fabrizio C Muredda, Andrea Bosin, Paolo Ruggerone, Alexandre M J J Bonvin, Attilio Vittorio Vargiu
Predicting binding events in very flexible, allosteric, multi-domain proteins. bioRxiv : the preprint server for biology (2024)
Marco Giulini, Rodrigo V Honorato, Jesús L Rivera, Alexandre M J J Bonvin
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information. Communications biology 7 (1) (2024)
Siri C van Keulen, Alexandre M J J Bonvin
Improving the quality of co-evolution intermolecular contact prediction with DisVis. Proteins (2023)
Yong Jung, Cunliang Geng, Alexandre M J J Bonvin, Li C Xue, Vasant G Honavar
MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations. Biomolecules 13 (1) (2023)
Yong Jung, Cunliang Geng, Alexandre M J J Bonvin, Li C Xue, Vasant G Honavar
MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations. Biomolecules 13 (1) (2023)
Yong Jung, Cunliang Geng, Alexandre M J J Bonvin, Li C Xue, Vasant G Honavar
MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations. Biomolecules 13 (1) (2023)
Felix van der Krift, Dick W Zijlmans, Rhythm Shukla, Ali Javed, Panagiotis I Koukos, Laura LE Schwarz, Elpetra Pm Timmermans-Sprang, Peter Em Maas, Digvijay Gahtory, Maurits van den Nieuwboer, Jan A Mol, Ger J Strous, Alexandre M J J Bonvin, Mario van der Stelt, Edwin J A Veldhuizen, Markus H Weingarth, Michiel Vermeulen, Judith Klumperman, Madelon M Maurice
A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance. Life science alliance 6 (11) (2023)
Marc F Lensink, Guillaume Brysbaert, Nessim Raouraoua, Paul A Bates, Marco Giulini, Rodrigo V Honorato, Charlotte van Noort, Joao M C Teixeira, Alexandre M J J Bonvin, Ren Kong, Hang Shi, Xufeng Lu, Shan Chang, Jian Liu, Zhiye Guo, Xiao Chen, Alex Morehead, Raj S Roy, Tianqi Wu, Nabin Giri, Farhan Quadir, Chen Chen, Jianlin Cheng, Carlos A Del Carpio, Eichiro Ichiishi, Luis A Rodriguez-Lumbreras, Juan Fernandez-Recio, Ameya Harmalkar, Lee-Shin Chu, Sam Canner, Rituparna Smanta, Jeffrey J Gray, Hao Li, Peicong Lin, Jiahua He, Huanyu Tao, Sheng-You Huang, Jorge Roel-Touris, Brian Jimenez-Garcia, Charles W Christoffer, Anika J Jain, Yuki Kagaya, Harini Kannan, Tsukasa Nakamura, Genki Terashi, Jacob C Verburgt, Yuanyuan Zhang, Zicong Zhang, Hayato Fujuta, Masakazu Sekijima, Daisuke Kihara, Omeir Khan, Sergei Kotelnikov, Usman Ghani, Dzmitry Padhorny, Dmitri Beglov, Sandor Vajda, Dima Kozakov, Surendra S Negi, Tiziana Ricciardelli, Didier Barradas-Bautista, Zhen Cao, Mohit Chawla, Luigi Cavallo, Romina Oliva, Rui Yin, Melyssa Cheung, Johnathan D Guest, Jessica Lee, Brian G Pierce, Ben Shor, Tomer Cohen, Matan Halfon, Dina Schneidman-Duhovny, Shaowen Zhu, Rujie Yin, Yuanfei Sun, Yang Shen, Martyna Maszota-Zieleniak, Krzysztof K Bojarski, Emilia A Lubecka, Mateusz Marcisz, Annemarie Danielsson, Lukasz Dziadek, Margrethe Gaardlos, Artur Gieldon, Adam Liwo, Sergey A Samsonov, Rafal Slusarz, Karolina Zieba, Adam K Sieradzan, Cezary Czaplewski, Shinpei Kobayashi, Yuta Miyakawa, Yasuomi Kiyota, Mayuko Takeda-Shitaka, Kliment Olechnovič, Lukas Valancauskas, Justas Dapkunas, Ceslovas Venclovas, Björn Wallner, Lin Yang, Chengyu Hou, Xiaodong He, Shuai Guo, Shenda Jiang, Xiaoliang Ma, Rui Duan, Liming Qui, Xianjin Xu, Xiaoqin Zou, Sameer Velankar, Shoshana J Wodak
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins (2023)
Yong Jung, Cunliang Geng, Alexandre M J J Bonvin, Li C Xue, Vasant G Honavar
MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations. Biomolecules 13 (1) (2023)
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, Jose M Ramos Pittol, Kedar Nath Natrajan, Sander Kersten, Frank C P Holstege, Houshang Monajemi, Saskia W C van Mil, Michiel Vermeulen, Birthe B Kragelund, David Cassiman, Susanne Mandrup, Eric Kalkhoven
PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation. Nature communications 13 (1) (2022)
Rhythm Shukla, Francesca Lavore, Sourav Maity, Maik G N Derks, Chelsea R Jones, Bram J A Vermeulen, Adéla Melcrová, Michael A Morris, Lea Marie Becker, Xiaoqi Wang, Raj Kumar, Joao Medeiros-Silva, Roy A M van Beekveld, Alexandre M J J Bonvin, Joseph Helmuth Lorent, Moreno Lelli, James S Nowick, Harold D MacGillavry, Aaron J Peoples, Amy L Spoering, Losee L Ling, Dallas E Hughes, Wouter H Roos, Eefjan Breukink, Kim Lewis, Markus H Weingarth
Teixobactin kills bacteria by a two-pronged attack on the cell envelope. Nature 608 (7922) (2022)
Vicky Charitou, Siri Camee van Keulen, Alexandre M J J Bonvin
Cyclization and Docking Protocol for Cyclic Peptide-Protein Modeling Using HADDOCK2.4. Journal of chemical theory and computation 18 (6) (2022)
Charles J Buchanan, Benjamin Gaunt, Peter J Harrison, Yun Yang, Jiwei Liu, Aziz Khan, Andrew M Giltrap, Audrey Le Bas, Philip N Ward, Kapil Gupta, Maud Dumoux, Tiong Kit Tan, Lisa Schimaski, Sergio Daga, Nicola Picchiotti, Margherita Baldassarri, Elisa Benetti, Chiara Fallerini, Francesca Fava, Annarita Giliberti, Panagiotis I Koukos, Matthew J Davy, Abirami Lakshminarayanan, Xiaochao Xue, Georgios Papadakis, Lachlan P Deimel, Virgínia Casablancas-Antràs, Timothy D W Claridge, Alexandre M J J Bonvin, Quentin J Sattentau, Simone Furini, Marco Gori, Jiandong Huo, Raymond J Owens, Christiane Schaffitzel, Imre Berger, Alessandra Renieri, null null, James H Naismith, Andrew J Baldwin, Benjamin G Davis
Pathogen-sugar interactions revealed by universal saturation transfer analysis. Science (New York, N.Y.) 377 (6604) (2022)
Zuzana Jandova, Attilio Vittorio Vargiu, Alexandre M J J Bonvin
Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue. Journal of chemical theory and computation 17 (9) (2021)
Alexandre M J J Bonvin
50 years of PBD: a catalyst in structural biology. Nature methods 18 (5) (2021)
Gytis Dudas, Samuel Leandro Hong, Barney I Potter, Sebastien Calvignac-Spencer, Frédéric S Niatou-Singa, Thais B Tombolomako, Terence Fuh-Neba, Ulrich Vickos, Markus Ulrich, Fabian Hubertus Leendertz, Kamran Khan, Carmen Huber, Alexander Watts, Ingrida Olendraitė, Joost Snijder, Kim N Wijnant, Alexandre M J J Bonvin, Pascale Martres, Sylvie Behillil, Ahidjo Ayouba, Martin Foudi Maidadi, Dowbiss Meta Djomsi, Celestin Godwe, Christelle Butel, Aistis Šimaitis, Migle Gabrielaite, Monika Katėnaitė, Rimvydas Norvilas, Ligita Raugaitė, Giscard Wilfried Koyaweda, Jephté Kaleb Kandou, Rimvydas Jonikas, Inga Nasvytienė, Živilė Žemeckienė, Dovydas Gečys, Kamilė Tamušauskaitė, Milda Norkienė, Emilija Vasiliūnaitė, Danguolė Žiogienė, Albertas Timinskas, Marius Šukys, Mantas Šarauskas, Gediminas Alzbutas, Adrienne Amuri Aziza, Eddy Kinganda Lusamaki, Jean-Claude Makangara Cigolo, Francisca Muyembe Mawete, Emmanuel Lokilo Lofiko, Placide Mbala Kingebeni, Jean-Jacques Muyembe Tamfum, Marie Roseline Darnycka Belizaire, René Ghislain Essomba, Marie Claire Okomo Assoumou, Akenji Blaise Mboringong, Alle Baba Dieng, Dovilė Juozapaitė, Salome Hosch, Justino Obama, Mitoha Ondo'o Ayekaba, Daniel Naumovas, Arnoldas Pautienius, Clotaire Donatien Rafaï, Astra Vitkauskienė, Rasa Ugenskienė, Alma Gedvilaitė, Darius Čereškevičius, Vaiva Lesauskaitė, Lukas Žemaitis, Laimonas Griškevičius, Guy Baele
Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Nature communications 12 (1) (2021)
Marc F Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael A G Chaleil, Tereza Clarence, Paul A Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Agnieszka G Lipska, Adam Liwo, Emilia A Lubecka, Martyna Maszota-Zieleniak, Adam K Sieradzan, Rafał Ślusarz, Patryk A Wesołowski, Karolina Zięba, Carlos A Del Carpio Muñoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J Gray, Alexandre M J J Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jiménez-García, Panagiotis I Koukos, Siri Van Keulen, Charlotte W Van Noort, Manon Réau, Jorge Roel-Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A Rodríguez-Lumbreras, Juan Fernández-Recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng-You Huang, Charles W Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G Pierce, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda-Shitaka, Petras J Kundrotas, Amar Singh, Ilya A Vakser, Justas Dapkunas, Kliment Olechnovič, Česlovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J Wodak
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins 89 (12) (2021)
Francesco Ambrosetti, Tobias Hegelund Olsen, Pier Paolo Olimpieri, Brian Jiménez-García, Edoardo Milanetti, Paolo Marcatilli, Alexandre M J J Bonvin
proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking. Bioinformatics (Oxford, England) 36 (20) (2021)
Nicolas Renaud, Cunliang Geng, Sonja Georgievska, Francesco Ambrosetti, Lars Ridder, Dario F Marzella, Manon F Réau, Alexandre M J J Bonvin, Li C Xue
DeepRank: a deep learning framework for data mining 3D protein-protein interfaces. Nature communications 12 (1) (2021)
Panagiotis I Koukos, Manon Réau, Alexandre M J J Bonvin
Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing. Journal of chemical information and modeling 61 (9) (2021)
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
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000Research 9 (2020)
Panagiotis I Koukos, Jorge Roel-Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E Trellet, Adrien S J Melquiond, Li C Xue, Rodrigo V Honorato, Irina Moreira, Zeynep Kurkcuoglu, Anna Vangone, Alexandre M J J Bonvin
An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45. Proteins 88 (8) (2020)
Jorge Roel-Touris, Brian Jiménez-García, Alexandre M J J Bonvin
Integrative modeling of membrane-associated protein assemblies. Nature communications 11 (1) (2020)
Rhythm Shukla, Joao Medeiros-Silva, Anish Parmar, Bram J A Vermeulen, Sanjit Das, Alessandra Lucini Paioni, Shehrazade Jekhmane, Joseph Helmuth Lorent, Alexandre M J J Bonvin, Marc Baldus, Moreno Lelli, Edwin J A Veldhuizen, Eefjan Breukink, Ishwar Singh, Markus H Weingarth
Mode of action of teixobactins in cellular membranes. Nature communications 11 (1) (2020)
Brian Jiménez-García, João M C Teixeira, Mikael E Trellet, João P G L M Rodrigues, Alexandre M J J Bonvin
PDB-tools web: A user-friendly interface for the manipulation of PDB files. Proteins 89 (3) (2020)
Huib H Rabouw, Linda J Visser, Tim Casper Passchier, Martijn A Langereis, Fan Liu, Piero Giansanti, Arno L W van Vliet, José G Dekker, Susanne G van der Grein, Jesús G Saucedo, Aditya A Anand, Mikael E Trellet, Alexandre M J J Bonvin, Peter Walter, Albert J R Heck, Raoul J de Groot, Frank J M van Kuppeveld
Inhibition of the integrated stress response by viral proteins that block p-eIF2-eIF2B association. Nature microbiology 5 (11) (2020)
Andrea Basciu, Panagiotis I Koukos, Giuliano Malloci, Alexandre M J J Bonvin, Attilio Vittorio Vargiu
Coupling enhanced sampling of the apo-receptor with template-based ligand conformers selection: performance in pose prediction in the D3R Grand Challenge 4. Journal of computer-aided molecular design 34 (2) (2019)
Zeynep Kurkcuoglu, Alexandre M J J Bonvin
Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems. Proteins 88 (2) (2019)
Teegan Lawson, Serene El-Kamand, Didier Boucher, Duc Cong Duong, Ruvini Kariawasam, Alexandre M J J Bonvin, Derek J Richard, Roland Gamsjaeger, Liza Cubeddu
The structural details of the interaction of single-stranded DNA binding protein hSSB2 (NABP1/OBFC2A) with UV-damaged DNA. Proteins 88 (2) (2019)
Leander Goldbach, Bram J A Vermeulen, Sami Caner, Minglong Liu, Christina Tysoe, Lieke van Gijzel, Ryoji Yoshisada, Mikael Trellet, Hugo van Ingen, Gary D Brayer, Alexandre M J J Bonvin, Seino A K Jongkees
Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic α-Amylase. ACS chemical biology 14 (8) (2019)
Andrea Basciu, Giuliano Malloci, Fabio Pietrucci, Alexandre M J J Bonvin, Attilio Vittorio Vargiu
Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape. Journal of chemical information and modeling 59 (4) (2019)
Mark Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M J J Bonvin, Matthieu Chavent, John D Chodera, Karmen Čondić-Jurkić, Lucie Delemotte, Helmut Grubmüller, Rebecca J Howard, E Joseph Jordan, Erik Lindahl, O H Samuli Ollila, Jana Selent, Daniel G A Smith, Phillip J Stansfeld, Johanna K S Tiemann, Mikael Trellet, Christopher Woods, Artem Zhmurov
Sharing Data from Molecular Simulations. Journal of chemical information and modeling 59 (10) (2019)
Jorge Roel-Touris, Charleen G Don, Rodrigo V Honorato, João P G L M Rodrigues, Alexandre M J J Bonvin
Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK. Journal of chemical theory and computation 15 (11) (2019)
Marc F Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphael A G Chaleil, Tereza Gerguri, Paul A Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran-Ran Liu, Xi-Ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov, Adam Liwo, Silvia Crivelli, Guillaume Pagès, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng-You Huang, Mireia Rosell, Luis A Rodríguez-Lumbreras, Miguel Romero-Durana, Lucía Díaz-Bueno, Juan Fernández-Recio, Charles W Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subraman, Daisuke Kihara, Dima Kozakov, Sandor Vajda, Kathryn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain H Moal, David W Ritchie, Isaure Chauvot de Beauchene, Bernard Maigret, Marie-Dominique Devignes, Maria E Ruiz Echartea, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yue Cao, Yang Shen, Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok, Merav Braitbard, Lirane Bitton, Dina Scheidman-Duhovny, Justas Dapkunas, Kliment Olechnovič, Česlovas Venclovas, Petras J Kundrotas, Saveliy Belkin, Devlina Chakravarty, Varsha D Badal, Ilya A Vakser, Thom Vreven, Sweta Vangaveti, Tyler Borrman, Nishigandha Phalke, Johnathan D Guest, Ragul Gowthaman, Brian G Pierce, Xianjin Xu, Rui Duan, Liming Qiu, Jie Hou, Benjamin Ryan Merideth, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Panagiotis I Koukos, Jorge Roel-Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E Trellet, Adrien S J Melquiond, Li Xue, Brian Jiménez-García, Charlotte W van Noort, Rodrigo V Honorato, Alexandre M J J Bonvin, Shoshana J Wodak
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins 87 (12) (2019)
João P G L M Rodrigues, João M C Teixeira, Mikaël Trellet, Alexandre M J J Bonvin
pdb-tools: a swiss army knife for molecular structures. F1000Research 7 (2018)
Winfried Roseboom, Madhvi G Nazir, Nils Y Meiresonne, Tamimount Mohammadi, Jolanda Verheul, Hansuk Buncherd, Alexandre M J J Bonvin, Leo J de Koning, Chris G de Koster, Luitzen de Jong, Tanneke den Blaauwen
Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis. International journal of molecular sciences 19 (10) (2018)
Cunliang Geng, Anna Vangone, Gert E Folkers, Li C Xue, Alexandre M J J Bonvin
iSEE: Interface structure, evolution, and energy-based machine learning predictor of binding affinity changes upon mutations. Proteins 87 (2) (2018)
Panagiotis I Koukos, Li C Xue, Alexandre M J J Bonvin
Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3. Journal of computer-aided molecular design 33 (1) (2018)
Jörg J Schaarschmidt, Bohdan Monastyrskyy, Andriy Kryshtafovych, Alexandre M J J Bonvin
Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age. Proteins (2017)
Ezgi Karaca, João P G L M Rodrigues, Andrea Graziadei, Alexandre M J J Bonvin, Teresa Carlomagno
M3: an integrative framework for structure determination of molecular machines. Nature methods 14 (9) (2017)
Irina S Moreira, Panagiotis I Koukos, Rita Melo, Jose G Almeida, Antonio J Preto, Joerg Schaarschmidt, Mikael E Trellet, Zeynep H Gümüş, Joaquim Costa, Alexandre M J J Bonvin
SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots. Scientific reports 7 (1) (2017)
Zeynep Kurkcuoglu, Panagiotis I Koukos, Nevia Citro, Mikael E Trellet, J P G L M Rodrigues, Irina S Moreira, Jorge Roel-Touris, Adrien S J Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C Xue, Anna Vangone, Alexandre M J J Bonvin
Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. Journal of computer-aided molecular design 32 (1) (2017)
Tanggis Bohnuud, Lingqi Luo, Shoshana J Wodak, Alexandre M J J Bonvin, Zhiping Weng, Sandor Vajda, Ora Schueler-Furman, Dima Kozakov
A benchmark testing ground for integrating homology modeling and protein docking. Proteins 85 (1) (2016)
A Vangone, J P G L M Rodrigues, L C Xue, G C P van Zundert, C Geng, Z Kurkcuoglu, M Nellen, S Narasimhan, E Karaca, M van Dijk, A S J Melquiond, Adrien S J Melquiond, M Trellet, P L Kastritis, Alexandre M J J Bonvin
Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1. Proteins 85 (3) (2016)
Renée C G de Bruin, Anita G M Stam, Anna Vangone, Paul M P van Bergen En Henegouwen, Henk M W Verheul, Zsolt Sebestyén, Jürgen Kuball, Alexandre M J J Bonvin, Tanja D de Gruijl, Hans J van der Vliet
Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody. Journal of immunology (Baltimore, Md. : 1950) 198 (1) (2016)
Marc F Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen-You Huang, Dina Schneidman-Duhovny, Andrej Sali, Joan Segura, Narcis Fernandez-Fuentes, Shruthi Viswanath, Ron Elber, Sergei Grudinin, Petr Popov, Emilie Neveu, Hasup Lee, Minkyung Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo Qin, Huan-Xiang Zhou, David W Ritchie, Bernard Maigret, Marie-Dominique Devignes, Anisah Ghoorah, Mieczyslaw Torchala, Raphaël A G Chaleil, Paul A Bates, Efrat Ben-Zeev, Miriam Eisenstein, Surendra S Negi, Zhiping Weng, Thom Vreven, Brian G Pierce, Tyler M Borrman, Jinchao Yu, Françoise Ochsenbein, Raphaël Guerois, Anna Vangone, João P G L M Rodrigues, Gydo van Zundert, Mehdi Nellen, Li Xue, Ezgi Karaca, Adrien S J Melquiond, Koen Visscher, Panagiotis L Kastritis, Alexandre M J J Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Shen, Lenna X Peterson, Hyung-Rae Kim, Amit Roy, Xusi Han, Juan Esquivel-Rodriguez, Daisuke Kihara, Xiaofeng Yu, Neil J Bruce, Jonathan C Fuller, Rebecca C Wade, Ivan Anishchenko, Petras J Kundrotas, Ilya A Vakser, Kenichiro Imai, Kazunori Yamada, Toshiyuki Oda, Tsukasa Nakamura, Kentaro Tomii, Chiara Pallara, Miguel Romero-Durana, Brian Jiménez-García, Iain H Moal, Juan Férnandez-Recio, Jong Young Joung, Jong Yun Kim, Keehyoung Joo, Jooyoung Lee, Dima Kozakov, Sandor Vajda, Scott Mottarella, David R Hall, Dmitri Beglov, Artem Mamonov, Bing Xia, Tanggis Bohnuud, Carlos A Del Carpio, Eichiro Ichiishi, Nicholas Marze, Daisuke Kuroda, Shourya S Roy Burman, Jeffrey J Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva, Andrey Tovchigrechko, Shoshana J Wodak
Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins (2016)
Gijs van der Schot, Alexandre M J J Bonvin
Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR. Journal of biomolecular NMR 62 (4) (2015)
Anna Vangone, Alexandre M J J Bonvin
Contacts-based prediction of binding affinity in protein-protein complexes. eLife 4 (2015)
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
Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife 3 (2014)

Alexandre M J J Bonvin.css-eqlu8i{font-size:small;padding-left:4px;} (A M J J Bonvin, Alexandre Mjj Bonvin)

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Alexandre M J J Bonvin (A M J J Bonvin, Alexandre Mjj Bonvin)