BioExcel Centre of Excellence for Computational Biomolecular Research

Informations projet

BioExcel-3

N° de convention de subvention: 101093290

DOI

10.3030/101093290

Date de signature de la CE 14 Decembre 2022

Date de début 1 Janvier 2023

Date de fin 31 Decembre 2026

Financé au titre de

• Digital, Industry and Space

Coût total

€ 5 873 754,50

Contribution de l’UE

€ 2 936 877,26

Coordonné par

KUNGLIGA TEKNISKA HOEGSKOLAN
Sweden

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Documents, reports (9)

Training Plan

This document will include an updated training needs analysis and an outline of the BioExcel Training programme.

Management Plan

Initial deliverable stating the management organization and planning for the entire project.

Updated software roadmaps

The roadmap for each of the core applications will be updated for new changes to HPC hardware and software contexts, user requests, and progress since previous roadmaps, including strategies to balance user requests with developer-identified software needs.

Dissemination and outreach plan

This document will outline the overall plan for dissemination and outreach activities of the CoE.

State-of-the-art and Initial Roadmap

This deliverable will summarise and describe the new technologies, methods and tools identified and collected to be used in the project workflows. From these, an initial roadmap will be proposed.

Collaboration plan

In collaboration with CASTIEL-2 CSA and complementary projects, the plan will identify synergies and common objectives for collaboration with EuroHPC JU HPC Centers, CoEs and CC. It will outline the activities and define related project-specific milestones. The collaboration plan will be updated whenever significant changes arise and before every periodic assessment of the project.

Report on User Support Processes

Description of established procedures for overall BioExcel-3 user support, including move of all support to BioExcel forums, mechanisms for users to provide input to user-driven development and how feedback is provided, publicly available information of how to join the Ambassador Program and plan for its activities, and summary of selected external showcases.

Data Management Plan

The plan will be developed in accordance with EC guidelines regarding FAIR data management and will describe what and how data will be generated, collected, processed, curated and preserved during and after the end of the project.

Quality assurance and risk management plan

This deliverable will discuss the overall quality monitoring process for the project (such as deliverables and milestone completion, KPIs) and the overall risk management strategy. The risks will be regularly assessed in the mandatory management reports.

Publications

Peer reviewed articles (44)

Resolving coupled pH titrations using alchemical free energy calculations

Auteurs: Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys
Publié dans: Journal of Computational Chemistry, Numéro 45, 2024, ISSN 0192-8651
Éditeur: Wiley
DOI: 10.1002/JCC.27318

Improved prediction of antibody and their complexes with clustered generative modelling ensembles

Auteurs: Xiaotong Xu, Marco Giulini, Alexandre M J J Bonvin
Publié dans: Bioinformatics Advances, Numéro 5, 2025, ISSN 2635-0041
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAF161

Flexibility in PAM recognition expands DNA targeting in xCas9

Auteurs: Kazi A Hossain, Lukasz Nierzwicki, Modesto Orozco, Jacek Czub, Giulia Palermo
Publié dans: eLife, Numéro 13, 2025, ISSN 2050-084X
Éditeur: eLife Sciences Publications, Ltd
DOI: 10.7554/ELIFE.102538.3

Molecular dynamics study of stiffness and rupture of axonal membranes

Auteurs: Maryam Majdolhosseini, Svein Kleiven, Alessandra Villa
Publié dans: Brain Research Bulletin, Numéro 223, 2025, ISSN 0361-9230
Éditeur: Elsevier BV
DOI: 10.1016/J.BRAINRESBULL.2025.111266

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

Auteurs: 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
Publié dans: Nature Protocols, Numéro 19, 2024, ISSN 2043-0116
Éditeur: Nature Publishing Group
DOI: 10.1038/S41596-024-01011-0

DeepRank-GNN-esm: A Graph Neural Network for Scoring Protein-Protein Models using Protein Language Model.

Auteurs: X. Xu, A.M.J.J. Bonvin
Publié dans: Bioinformatics Advances, 2023, ISSN 2635-0041
Éditeur: Oxford Academic
DOI: 10.1093/bioadv/vbad191

The SH protein of mumps virus is a druggable pentameric viroporin

Auteurs: Kira Devantier, Trine L. Toft-Bertelsen, Andreas Prestel, Viktoria M. S. Kjær, Cagla Sahin, Marco Giulini, Stavroula Louka, Katja Spiess, Asmita Manandhar, Katrine Qvortrup, Trond Ulven, Bo H. Bentzen, Alexandre MJJ Bonvin, Nanna MacAulay, Birthe B. Kragelund, Mette M. Rosenkilde
Publié dans: Science Advances, Numéro 11, 2025, ISSN 2375-2548
Éditeur: American Association for the Advancement of Science (AAAS)
DOI: 10.1126/SCIADV.ADS3071

A new paradigm for molecular dynamics databases: the COVID-19 database, the legacy of a titanic community effort

Auteurs: Daniel Beltrán; Adam Hospital; Josep Lluís Gelpí; Modesto Orozco
Publié dans: Nucleic Acids Research, 2023, ISSN 1362-4962
Éditeur: Oxford University Press
DOI: 10.1093/NAR/GKAD991

Modeling Protein–Glycan Interactions with HADDOCK

Auteurs: Anna Ranaudo, Marco Giulini, Angela Pelissou Ayuso, Alexandre M. J. J. Bonvin
Publié dans: Journal of Chemical Information and Modeling, Numéro 64, 2024, ISSN 1549-9596
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.4C01372

Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange

Auteurs: Matthew L. Evans; Johan Bergsma; Andrius Merkys; Casper W. Andersen; Oskar B. Andersson; Daniel Beltrán; Evgeny Blokhin; Tara M. Boland; Rubén Castañeda Balderas; Kamal Choudhary; Alberto Díaz Díaz; Rodrigo Domínguez García; Hagen Eckert; Kristjan Eimre; María Elena Fuentes Montero; Adam M. Krajewski; Jens Jørgen Mortensen; José Manuel Nápoles Duarte; Jacob Pietryga; Ji Qi; Felipe de Jesús Trejo Carrillo; Antanas Vaitkus; Jusong Yu; Adam Zettel; Pedro Baptista de Castro; Johan Carlsson; Tiago F. T. Cerqueira; Simon Divilov; Hamidreza Hajiyani; Felix Hanke; Kevin Jose; Corey Oses; Janosh Riebesell; Jonathan Schmidt; Donald Winston; Christen Xie; Xiaoyu Yang; Sara Bonella; Silvana Botti; Stefano Curtarolo; Claudia Draxl; Luis Edmundo Fuentes Cobas; Adam Hospital; Zi-Kui Liu; Miguel A. L. Marques; Nicola Marzari; Andrew J. Morris; Shyue Ping Ong; Modesto Orozco; Kristin A. Persson; Kristian S. Thygesen; Chris Wolverton; Markus Scheidgen; Cormac Toher; Gareth J. Conduit; Giovanni Pizzi; Saulius Gražulis; Gian-Marco Rignanese; Rickard Armiento
Publié dans: Digital Discovery, 2024, ISSN 2635-098X
Éditeur: Royal Society of Chemistry (RSC)
DOI: 10.48550/ARXIV.2402.00572

CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes

Auteurs: David Farré-Gil, Juan Pablo Arcon, Charles A Laughton, Modesto Orozco
Publié dans: Nucleic Acids Research, Numéro 52, 2024, ISSN 0305-1048
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAE444

MDverse, shedding light on the dark matter of molecular dynamics simulations

Auteurs: Johanna KS Tiemann, Magdalena Szczuka, Lisa Bouarroudj, Mohamed Oussaren, Steven Garcia, Rebecca J Howard, Lucie Delemotte, Erik Lindahl, Marc Baaden, Kresten Lindorff-Larsen, Matthieu Chavent, Pierre Poulain
Publié dans: eLife, Numéro 12, 2024, ISSN 2050-084X
Éditeur: eLife Sciences Publications, Ltd
DOI: 10.7554/ELIFE.90061.3

HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes

Auteurs: Marco Giulini, Victor Reys, João M. C. Teixeira, Brian Jiménez-García, Rodrigo V. Honorato, Anna Kravchenko, Xiaotong Xu, Raphaëlle Versini, Anna Engel, Stefan Verhoeven, Alexandre M. J. J. Bonvin
Publié dans: Journal of Chemical Information and Modeling, Numéro 65, 2025, ISSN 1549-9596
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.5C00969

Accurately Predicting Protein p<i>K</i>_a Values Using Nonequilibrium Alchemy

Auteurs: Carter J. Wilson, Mikko Karttunen, Bert L. de Groot, Vytautas Gapsys
Publié dans: Journal of Chemical Theory and Computation, Numéro 19, 2023, ISSN 1549-9618
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.3C00721

The need to implement FAIR principles in biomolecular simulations

Auteurs: Rommie E. Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Daniel Beltran, Philip C. Biggin, Massimiliano Bonomi, Gregory R. Bowman, Richard A. Bryce, Giovanni Bussi, Paolo Carloni, David A. Case, Andrea Cavalli, Chia-En A. Chang, Thomas E. Cheatham, Margaret S. Cheung, Christophe Chipot, Lillian T. Chong, Preeti Choudhary, G. Andres Cisneros, Cecilia Clementi, Rosana Collepardo-Guevara, Peter Coveney, Roberto Covino, T. Daniel Crawford, Matteo Dal Peraro, Bert L. de Groot, Lucie Delemotte, Marco De Vivo, Jonathan W. Essex, Franca Fraternali, Jiali Gao, Josep Ll. Gelpí, Francesco L. Gervasio, Fernando D. González-Nilo, Helmut Grubmüller, Marina G. Guenza, Horacio V. Guzman, Sarah Harris, Teresa Head-Gordon, Rigoberto Hernandez, Adam Hospital, Niu Huang, Xuhui Huang, Gerhard Hummer, Javier Iglesias-Fernández, Jan H. Jensen, Shantenu Jha, Wanting Jiao, William L. Jorgensen, Shina C. L. Kamerlin, Syma Khalid, Charles Laughton, Michael Levitt, Vittorio Limongelli, Erik Lindahl, Kresten Lindorff-Larsen, Sharon Loverde, Magnus Lundborg, Yun L. Luo, F. Javier Luque, Charlotte I. Lynch, Alexander D. MacKerell, Alessandra Magistrato, Siewert J. Marrink, Hugh Martin, J. Andrew McCammon, Kenneth Merz, Vicent Moliner, Adrian J. Mulholland, Sohail Murad, Athi N. Naganathan, Shikha Nangia, Frank Noe, Agnes Noy, Julianna Oláh, Megan L. O’Mara, Mary Jo Ondrechen, Jose N. Onuchic, Alexey Onufriev, Sílvia Osuna, Giulia Palermo, Anna R. Panchenko, Sergio Pantano, Carol Parish, Michele Parrinello, Alberto Perez, Tomas Perez-Acle, Juan R. Perilla, B. Montgomery Pettitt, Adriana Pietropaolo, Jean-Philip Piquemal, Adolfo B. Poma, Matej Praprotnik, Maria J. Ramos, Pengyu Ren, Nathalie Reuter, Adrian Roitberg, Edina Rosta, Carme Rovira, Benoit Roux, Ursula Rothlisberger, Karissa Y. Sanbonmatsu, Tamar Schlick, Alexey K. Shaytan, Carlos Simmerling, Jeremy C. Smith, Yuji Sugita, Katarzyna Świderek, Makoto Taiji, Peng Tao, D. Peter Tieleman, Irina G. Tikhonova, Julian Tirado-Rives, Iñaki Tuñón, Marc W. van der Kamp, David van der Spoel, Sameer Velankar, Gregory A. Voth, Rebecca Wade, Ariel Warshel, Valerie Vaissier Welborn, Stacey D. Wetmore, Travis J. Wheeler, Chung F. Wong, Lee-Wei Yang, Martin Zacharias, Modesto Orozco
Publié dans: Nature Methods, Numéro 22, 2025, ISSN 1548-7091
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/S41592-025-02635-0

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

Auteurs: M. Giulini, C. Schneider, D. Cutting, N. Desai, C. Deane and A.M.J.J. Bonvin
Publié dans: BioRxiv, 2023, ISSN 2692-8205
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.17.567543

Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides

Auteurs: Vito Genna, Javier Iglesias-Fernández, et al.,
Publié dans: Nucleic Acids Research, 2023, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/NAR/GKAD309

An integrated machine-learning model to predict nucleosome architecture

Auteurs: Alba Sala, Mireia Labrador, Diana Buitrago, Pau De Jorge, Federica Battistini, Isabelle Brun Heath, Modesto Orozco
Publié dans: Nucleic Acids Research, Numéro 52, 2024, ISSN 0305-1048
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAE689

The conserved lysine residue in transmembrane helix 5 is pivotal for the cytoplasmic gating of the <scp>L-</scp>amino acid transporters

Auteurs: Joana Fort, Adrià Nicolàs-Aragó, Luca Maggi, Maria Martinez-Molledo, Despoina Kapiki, Paula González-Novoa, Patricia Gómez-Gejo, Niels Zijlstra, Susanna Bodoy, Els Pardon, Jan Steyaert, Oscar Llorca, Modesto Orozco, Thorben Cordes, Manuel Palacín
Publié dans: PNAS Nexus, Numéro 4, 2025, ISSN 2752-6542
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/PNASNEXUS/PGAE584

IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods

Auteurs: Brinda Vallat, Benjamin M. Webb, John D. Westbrook, Thomas D. Goddard, Christian A. Hanke, Andrea Graziadei, Ezra Peisach, Arthur Zalevsky, Jared Sagendorf, Hongsuda Tangmunarunkit, Serban Voinea, Monica Sekharan, Jian Yu, Alexander A.M.J.J. Bonvin, Frank DiMaio, Gerhard Hummer, Jens Meiler, Emad Tajkhorshid, Thomas E. Ferrin, Catherine L. Lawson, Alexander Leitner, Juri Rappsilber, Claus A.M. Seidel, Cy M. Jeffries, Stephen K. Burley, Jeffrey C. Hoch, Genji Kurisu, Kyle Morris, Ardan Patwardhan, Sameer Velankar, Torsten Schwede, Jill Trewhella, Carl Kesselman, Helen M. Berman, Andrej Sali
Publié dans: Journal of Molecular Biology, Numéro 436, 2024, ISSN 0022-2836
Éditeur: Elsevier BV
DOI: 10.1016/J.JMB.2024.168546

Integrative Modeling in the Age of Machine Learning: A Summary of <scp>HADDOCK</scp> Strategies in <scp>CAPRI</scp> Rounds 47–55

Auteurs: Victor Reys, Marco Giulini, Vlad Cojocaru, Anna Engel, Xiaotong Xu, Jorge Roel‐Touris, Cunliang Geng, Francesco Ambrosetti, Brian Jiménez‐García, Zuzana Jandova, Panagiotis I. Koukos, Charlotte van Noort, João M. C. Teixeira, Siri C. van Keulen, Manon Réau, Rodrigo V. Honorato, Alexandre M. J. J. Bonvin
Publié dans: Proteins: Structure, Function, and Bioinformatics, 2024, ISSN 0887-3585
Éditeur: Wiley
DOI: 10.1002/PROT.26789

Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism

Auteurs: Vito Genna, Guillem Portella, Alba Sala, Montserrat Terrazas, Israel Serrano-Chacón, Javier González, Núria Villegas, Lidia Mateo, Chiara Castellazzi, Mireia Labrador, Anna Aviño, Adam Hospital, Albert Gandioso, Patrick Aloy, Isabelle Brun-Heath, Carlos Gonzalez, Ramon Eritja, Modesto Orozco
Publié dans: Nucleic Acids Research, Numéro 53, 2025, ISSN 0305-1048
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAF170

Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins

Auteurs: Andrea Basciu, Mohd Athar, Han Kurt, Christine Neville, Giuliano Malloci, Fabrizio C. Muredda, Andrea Bosin, Paolo Ruggerone, Alexandre M. J. J. Bonvin, Attilio V. Vargiu
Publié dans: Journal of Chemical Information and Modeling, Numéro 65, 2025, ISSN 1549-9596
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.4C01810

Formation of left-handed helices by C2′-fluorinated nucleic acids under physiological salt conditions

Auteurs: Roberto El-Khoury, Cristina Cabrero, Santiago Movilla, Harneesh Kaur, David Friedland, Arnau Domínguez, James D Thorpe, Morgane Roman, Modesto Orozco, Carlos González, Masad J Damha
Publié dans: Nucleic Acids Research, Numéro 52, 2024, ISSN 0305-1048
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAE508

ARCTIC-3D: Automatic Retrieval and ClusTering of Interfaces in Complexes from 3D structural information

Auteurs: Marco Giulini; Rodrigo V. Honorato; Jesús L. Rivera; Alexandre M.J.J. Bonvin
Publié dans: Communication Biology, Numéro 7:49, 2024, ISSN 2399-3642
Éditeur: Springer Nature
DOI: 10.5281/zenodo.8131700

Main role of fractal-like nature of conformational space in subdiffusion in proteins

Auteurs: Luca Maggi, Modesto Orozco
Publié dans: Physical Review E, Numéro 109, 2024, ISSN 2470-0045
Éditeur: American Physical Society (APS)
DOI: 10.1103/PHYSREVE.109.034402

Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy

Auteurs: Sudarshan Behera, David F. Hahn, Carter J. Wilson, Simone Marsili, Gary Tresadern, Vytautas Gapsys, Bert L. de Groot
Publié dans: Journal of Chemical Information and Modeling, Numéro 65, 2025, ISSN 1549-9596
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.5C00947

Molecular determinants for recognition of serotonylated chromatin

Auteurs: Laura Pulido-Cortés, Hajo Gielingh, Vito Thijssen, Minglong Liu, Ryoji Yoshisada, Leonardo Romão Soares, Sheikh Nizamuddin, Florian Friedrich, Holger Greschik, Ling Peng, Rodrigo Vargas Honorato, Manfred Jung, Alexandre M J J Bonvin, Martin L Biniossek, Roland Schüle, Seino Jongkees, Hugo van Ingen, H Th Marc Timmers
Publié dans: Nucleic Acids Research, Numéro 53, 2025, ISSN 0305-1048
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAF612

Structural analysis of the Candida albicans mitochondrial DNA maintenance factor Gcf1p reveals a dynamic DNA-bridging mechanism

Auteurs: Aleix Tarrés-Solé, Federica Battistini, Joachim M Gerhold, Olivier Piétrement, Belén Martínez-García, Elena Ruiz-López, Sébastien Lyonnais, Pau Bernadó, Joaquim Roca, Modesto Orozco, Eric Le Cam, Juhan Sedman, Maria Solà
Publié dans: Nucleic Acids Research, 2023, ISSN 1362-4962
Éditeur: Oxford University Press
DOI: 10.1093/NAR/GKAD397

Biomolecular Interaction Prediction in the Pre‐ and Post‐<scp>AlphaFold</scp> Era: The 8th <scp>CAPRI</scp> Evaluation

Auteurs: Marc F. Lensink, Nessim Raouraoua, Guillaume Brysbaert, Sameer Velankar, Shoshana J. Wodak, Alexandre M. J. J. Bonvin
Publié dans: Proteins: Structure, Function, and Bioinformatics, 2025, ISSN 0887-3585
Éditeur: Wiley
DOI: 10.1002/PROT.70018

Accelerating protein–protein interaction screens with reduced AlphaFold-Multimer sampling

Auteurs: Greta Bellinzona, Davide Sassera, Alexandre M J J Bonvin
Publié dans: Bioinformatics Advances, Numéro 4, 2024, ISSN 2635-0041
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAE153

The Rhodium Analogue of Coenzyme B₁₂ as an Anti‐Photoregulatory Ligand Inhibiting Bacterial CarH Photoreceptors

Auteurs: Ricardo Pérez‐Castaño, Juan Aranda, Florian J. Widner, Christoph Kieninger, Evelyne Deery, Martin J. Warren, Modesto Orozco, Montserrat Elías‐Arnanz, S. Padmanabhan, Bernhard Kräutler
Publié dans: Angewandte Chemie International Edition, Numéro 63, 2024, ISSN 1433-7851
Éditeur: Wiley
DOI: 10.1002/ANIE.202401626

Site-specific incorporation of a fluorescent nucleobase analog enhances i-motif stability and allows monitoring of i-motif folding inside cells

Auteurs: Bartomeu Mir, Israel Serrano-Chacón, Pedro Medina, Veronica Macaluso, Montserrat Terrazas, Albert Gandioso, Miguel Garavís, Modesto Orozco, Núria Escaja, Carlos González
Publié dans: Nucleic Acids Research, Numéro 52, 2024, ISSN 0305-1048
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAE106

<scp>Pre‐exascale HPC</scp> approaches for molecular dynamics simulations. Covid‐19 research: A use case

Auteurs: Miłosz Wieczór, Vito Genna, Juan Aranda, Rosa M. Badia, Josep Lluís Gelpí, Vytautas Gapsys, Bert L. de Groot, Erik Lindahl, Martí Municoy, Adam Hospital, Modesto Orozco
Publié dans: WIREs Computational Molecular Science, Numéro 13, 2023, ISSN 1759-0876
Éditeur: Wiley
DOI: 10.1002/WCMS.1622

Characterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway

Auteurs: González, L., Díaz, L., Pous, J. et al.
Publié dans: Nature Communications, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/S41467-023-39051-X

Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows

Auteurs: Bayarri, Genís; Andrio, Pau; Gelpi, Josep; Hospital, Adam; Orozco, Modesto
Publié dans: PLOS Computational Biology, 2024, ISSN 1553-7358
Éditeur: Public Library of Science (PLoS)
DOI: 10.1371/JOURNAL.PCBI.1012173

DeepRank-GNN: A Graph Neural Network Framework to Learn Patterns in Protein-Protein Interfaces

Auteurs: M.F. Réau, N.Renaud, L.C. Xue and A.M.J.J. Bonvin
Publié dans: Bioinformatics, 2023, ISSN 1367-4811
Éditeur: Oxford Academic
DOI: 10.1093/bioinformatics/btac759

CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers

Auteurs: David Farré-Gil, Genis Bayarri, Charles A Laughton, Adam Hospital, Modesto Orozco
Publié dans: Nucleic Acids Research, Numéro 53, 2025, ISSN 0305-1048
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAF371

Angewandte Chemie - International Edition

Auteurs: Ricardo Pérez‐Castaño; Juan Aranda; Florian J. Widner; Christoph Kieninger; Evelyne Deery; Martin J. Warren; Modesto Orozco; Montserrat Elías‐Arnanz; S. Padmanabhan; Bernhard Kräutler
Publié dans: Angewandte Chemie International Edition, 2024, ISSN 1433-7851
Éditeur: SAGE Publications Ltd
DOI: 10.1002/ANGE.202401626

Correlated motions in DNA: beyond base-pair step models of DNA flexibility

Auteurs: Kim López-Güell, Federica Battistini, Modesto Orozco
Publié dans: Nucleic Acids Research, 2023, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/NAR/GKAD136

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

Auteurs: Marco Giulini; Constantin Schneider; Daniel Cutting; Nikita Desai; Charlotte M. Deane; Alexandre M.J.J. Bonvin
Publié dans: Bioinformatics, Numéro 40, 2024, ISSN 1367-4811
Éditeur: Oxford Press
DOI: 10.1101/2023.11.17.567543

i-Motif folding intermediates with zero-nucleotide loops are trapped by 2′-fluoroarabinocytidine via F···H and O···H hydrogen bonds

Auteurs: El-Khoury, R., Macaluso, V., Hennecker, C. et al
Publié dans: Communications Chemistry, 2023, ISSN 2399-3669
Éditeur: Communications Chemistry (Commun Chem)
DOI: 10.1038/S42004-023-00831-7

Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA

Auteurs: Rodriguez J, Battistini F, Learte-Aymamí S, Orozco M, Mascareñas JL.
Publié dans: RSC Chem Biol., 2023, ISSN 2633-0679
Éditeur: Royal Society of Chemistry
DOI: 10.1039/D3CB00053B

Guidelines for Free-Energy Calculations Involving Charge Changes

Auteurs: Drazen Petrov, Jan Walther Perthold, Chris Oostenbrink, Bert L. de Groot, Vytautas Gapsys
Publié dans: Journal of Chemical Theory and Computation, Numéro 20, 2024, ISSN 1549-9618
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.3C00757