BioExcel Centre of Excellence for Computational Biomolecular Research

Informazioni relative al progetto

BioExcel-3

ID dell’accordo di sovvenzione: 101093290

DOI

10.3030/101093290

Data della firma CE 14 Dicembre 2022

Data di avvio 1 Gennaio 2023

Data di completamento 31 Dicembre 2026

Finanziato da

• Digital, Industry and Space

Costo totale

€ 5 873 754,50

Contributo UE

€ 2 936 877,26

Coordinato da

KUNGLIGA TEKNISKA HOEGSKOLAN
Sweden

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

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.

Pubblicazioni

Peer reviewed articles (44)

Resolving coupled pH titrations using alchemical free energy calculations

Autori: Carter J. Wilson, Bert L. de Groot, Vytautas Gapsys
Pubblicato in: Journal of Computational Chemistry, Numero 45, 2024, ISSN 0192-8651
Editore: Wiley
DOI: 10.1002/JCC.27318

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

Autori: Xiaotong Xu, Marco Giulini, Alexandre M J J Bonvin
Pubblicato in: Bioinformatics Advances, Numero 5, 2025, ISSN 2635-0041
Editore: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAF161

Flexibility in PAM recognition expands DNA targeting in xCas9

Autori: Kazi A Hossain, Lukasz Nierzwicki, Modesto Orozco, Jacek Czub, Giulia Palermo
Pubblicato in: eLife, Numero 13, 2025, ISSN 2050-084X
Editore: eLife Sciences Publications, Ltd
DOI: 10.7554/ELIFE.102538.3

Molecular dynamics study of stiffness and rupture of axonal membranes

Autori: Maryam Majdolhosseini, Svein Kleiven, Alessandra Villa
Pubblicato in: Brain Research Bulletin, Numero 223, 2025, ISSN 0361-9230
Editore: Elsevier BV
DOI: 10.1016/J.BRAINRESBULL.2025.111266

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

Autori: 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
Pubblicato in: Nature Protocols, Numero 19, 2024, ISSN 2043-0116
Editore: 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.

Autori: X. Xu, A.M.J.J. Bonvin
Pubblicato in: Bioinformatics Advances, 2023, ISSN 2635-0041
Editore: Oxford Academic
DOI: 10.1093/bioadv/vbad191

The SH protein of mumps virus is a druggable pentameric viroporin

Autori: 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
Pubblicato in: Science Advances, Numero 11, 2025, ISSN 2375-2548
Editore: 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

Autori: Daniel Beltrán; Adam Hospital; Josep Lluís Gelpí; Modesto Orozco
Pubblicato in: Nucleic Acids Research, 2023, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/NAR/GKAD991

Modeling Protein–Glycan Interactions with HADDOCK

Autori: Anna Ranaudo, Marco Giulini, Angela Pelissou Ayuso, Alexandre M. J. J. Bonvin
Pubblicato in: Journal of Chemical Information and Modeling, Numero 64, 2024, ISSN 1549-9596
Editore: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.4C01372

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

Autori: 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
Pubblicato in: Digital Discovery, 2024, ISSN 2635-098X
Editore: 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

Autori: David Farré-Gil, Juan Pablo Arcon, Charles A Laughton, Modesto Orozco
Pubblicato in: Nucleic Acids Research, Numero 52, 2024, ISSN 0305-1048
Editore: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAE444

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

Autori: 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
Pubblicato in: eLife, Numero 12, 2024, ISSN 2050-084X
Editore: eLife Sciences Publications, Ltd
DOI: 10.7554/ELIFE.90061.3

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

Autori: 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
Pubblicato in: Journal of Chemical Information and Modeling, Numero 65, 2025, ISSN 1549-9596
Editore: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.5C00969

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

Autori: Carter J. Wilson, Mikko Karttunen, Bert L. de Groot, Vytautas Gapsys
Pubblicato in: Journal of Chemical Theory and Computation, Numero 19, 2023, ISSN 1549-9618
Editore: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.3C00721

The need to implement FAIR principles in biomolecular simulations

Autori: 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
Pubblicato in: Nature Methods, Numero 22, 2025, ISSN 1548-7091
Editore: 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.

Autori: M. Giulini, C. Schneider, D. Cutting, N. Desai, C. Deane and A.M.J.J. Bonvin
Pubblicato in: BioRxiv, 2023, ISSN 2692-8205
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.17.567543

Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides

Autori: Vito Genna, Javier Iglesias-Fernández, et al.,
Pubblicato in: Nucleic Acids Research, 2023, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/NAR/GKAD309

An integrated machine-learning model to predict nucleosome architecture

Autori: Alba Sala, Mireia Labrador, Diana Buitrago, Pau De Jorge, Federica Battistini, Isabelle Brun Heath, Modesto Orozco
Pubblicato in: Nucleic Acids Research, Numero 52, 2024, ISSN 0305-1048
Editore: 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

Autori: 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
Pubblicato in: PNAS Nexus, Numero 4, 2025, ISSN 2752-6542
Editore: Oxford University Press (OUP)
DOI: 10.1093/PNASNEXUS/PGAE584

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

Autori: 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
Pubblicato in: Journal of Molecular Biology, Numero 436, 2024, ISSN 0022-2836
Editore: 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

Autori: 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
Pubblicato in: Proteins: Structure, Function, and Bioinformatics, 2024, ISSN 0887-3585
Editore: Wiley
DOI: 10.1002/PROT.26789

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

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 53, 2025, ISSN 0305-1048
Editore: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAF170

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

Autori: 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
Pubblicato in: Journal of Chemical Information and Modeling, Numero 65, 2025, ISSN 1549-9596
Editore: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCIM.4C01810

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

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 52, 2024, ISSN 0305-1048
Editore: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAE508

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

Autori: Marco Giulini; Rodrigo V. Honorato; Jesús L. Rivera; Alexandre M.J.J. Bonvin
Pubblicato in: Communication Biology, Numero 7:49, 2024, ISSN 2399-3642
Editore: Springer Nature
DOI: 10.5281/zenodo.8131700

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

Autori: Luca Maggi, Modesto Orozco
Pubblicato in: Physical Review E, Numero 109, 2024, ISSN 2470-0045
Editore: American Physical Society (APS)
DOI: 10.1103/PHYSREVE.109.034402

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

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

Molecular determinants for recognition of serotonylated chromatin

Autori: 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
Pubblicato in: Nucleic Acids Research, Numero 53, 2025, ISSN 0305-1048
Editore: 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

Autori: 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
Pubblicato in: Nucleic Acids Research, 2023, ISSN 1362-4962
Editore: 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

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

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

Autori: Greta Bellinzona, Davide Sassera, Alexandre M J J Bonvin
Pubblicato in: Bioinformatics Advances, Numero 4, 2024, ISSN 2635-0041
Editore: Oxford University Press (OUP)
DOI: 10.1093/BIOADV/VBAE153

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

Autori: Ricardo Pérez‐Castaño, Juan Aranda, Florian J. Widner, Christoph Kieninger, Evelyne Deery, Martin J. Warren, Modesto Orozco, Montserrat Elías‐Arnanz, S. Padmanabhan, Bernhard Kräutler
Pubblicato in: Angewandte Chemie International Edition, Numero 63, 2024, ISSN 1433-7851
Editore: 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

Autori: Bartomeu Mir, Israel Serrano-Chacón, Pedro Medina, Veronica Macaluso, Montserrat Terrazas, Albert Gandioso, Miguel Garavís, Modesto Orozco, Núria Escaja, Carlos González
Pubblicato in: Nucleic Acids Research, Numero 52, 2024, ISSN 0305-1048
Editore: 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

Autori: 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
Pubblicato in: WIREs Computational Molecular Science, Numero 13, 2023, ISSN 1759-0876
Editore: Wiley
DOI: 10.1002/WCMS.1622

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

Autori: González, L., Díaz, L., Pous, J. et al.
Pubblicato in: Nature Communications, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/S41467-023-39051-X

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

Autori: Bayarri, Genís; Andrio, Pau; Gelpi, Josep; Hospital, Adam; Orozco, Modesto
Pubblicato in: PLOS Computational Biology, 2024, ISSN 1553-7358
Editore: 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

Autori: M.F. Réau, N.Renaud, L.C. Xue and A.M.J.J. Bonvin
Pubblicato in: Bioinformatics, 2023, ISSN 1367-4811
Editore: Oxford Academic
DOI: 10.1093/bioinformatics/btac759

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

Autori: David Farré-Gil, Genis Bayarri, Charles A Laughton, Adam Hospital, Modesto Orozco
Pubblicato in: Nucleic Acids Research, Numero 53, 2025, ISSN 0305-1048
Editore: Oxford University Press (OUP)
DOI: 10.1093/NAR/GKAF371

Angewandte Chemie - International Edition

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

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

Autori: Kim López-Güell, Federica Battistini, Modesto Orozco
Pubblicato in: Nucleic Acids Research, 2023, ISSN 0305-1048
Editore: 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

Autori: Marco Giulini; Constantin Schneider; Daniel Cutting; Nikita Desai; Charlotte M. Deane; Alexandre M.J.J. Bonvin
Pubblicato in: Bioinformatics, Numero 40, 2024, ISSN 1367-4811
Editore: 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

Autori: El-Khoury, R., Macaluso, V., Hennecker, C. et al
Pubblicato in: Communications Chemistry, 2023, ISSN 2399-3669
Editore: 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

Autori: Rodriguez J, Battistini F, Learte-Aymamí S, Orozco M, Mascareñas JL.
Pubblicato in: RSC Chem Biol., 2023, ISSN 2633-0679
Editore: Royal Society of Chemistry
DOI: 10.1039/D3CB00053B

Guidelines for Free-Energy Calculations Involving Charge Changes

Autori: Drazen Petrov, Jan Walther Perthold, Chris Oostenbrink, Bert L. de Groot, Vytautas Gapsys
Pubblicato in: Journal of Chemical Theory and Computation, Numero 20, 2024, ISSN 1549-9618
Editore: American Chemical Society (ACS)
DOI: 10.1021/ACS.JCTC.3C00757