From fragments to high affinity binders interfacing integrated structural biology, medicinal chemistry and artificial intelligence

Projektinformationen

Fragment-Screen

ID Finanzhilfevereinbarung: 101094131

DOI

10.3030/101094131

EK-Unterschriftsdatum 13 Dezember 2022

Startdatum 1 Februar 2023

Enddatum 31 Januar 2026

Finanziert unter

• Research infrastructures

Gesamtkosten

€ 8 265 079,64

EU-Beitrag

€ 8 265 079,64

Koordiniert durch

INSTRUCT-ERIC
United Kingdom

CORDIS bietet Links zu öffentlichen Ergebnissen und Veröffentlichungen von HORIZONT-Projekten.

Links zu Ergebnissen und Veröffentlichungen von RP7-Projekten sowie Links zu einigen Typen spezifischer Ergebnisse wie Datensätzen und Software werden dynamisch von OpenAIRE abgerufen.

Leistungen

Documents, reports (10)

Proof of concept for in situ room temperature FBDD at DLS

Report on in situ room temperature fragment based drug discovery at DLS

Definition and pilot implementation of data/metadata standards for FBDD-NMR

First analysis of the metafa for FBDD-NMR to be used in the project, together with their initial data management software

Map of training needs and competencies of the consortium

Report on training needs of the consortium partners, the skills of consortium partners and a gap analysis

ARIA enhancements for exploitation of new technologies

Report on changes to ARIA access management software towards better use of the new technologies

Native MS validation screens

Completion of first detailed validation screens from native MS

Interoperability of Fragalysis with existing workflows

Report on interoperability of workflows with Fragalysis

Make AI tools developed under task 6.1 available to the scientific community

AI tools and documentations developed will be made available to the community through open-source platform at https://github.com/IBM/AIBinder.

Detailed methods and protocols in place for medium throughput of fragment binding and binding location by MRMS native MS and top-down

Protocol for fragment binding, including sample preparation and instrumental parameters

Website and social media setup

Launch project website and social media channels

Communication Plan

Communication plan with proposed outreach activities within the Fragment-Screen project

Data Management Plan (1)

Project handbook and Data Management Plan

Publish a handbook documenting the project management processes, branding, and general project information for use by the consortium members. The handbook will include the project’s data management plan, specifying which type of data will be dealt with, and how they will meet FAIR principles to allow for their re-use for research.

Demonstrators, pilots, prototypes (1)

Pilot open, FAIR repository with FBDD datasets made available

First implementation of FBDD repository, coordinated by EBI

Veröffentlichungen

Book chapters (1)

Language Models in Molecular Discovery

Autoren: Nikita Janakarajan, Tim Erdmann, Sarath Swaminathan, Teodoro Laino, Jannis Born
Veröffentlicht in: Drug Development Supported by Informatics, 2024
Herausgeber: Springer Nature Singapore
DOI: 10.1007/978-981-97-4828-0_7

Peer reviewed articles (12)

Regression Transformer enables concurrent sequence regression and generation for molecular language modelling

Autoren: Jannis Born, Matteo Manica
Veröffentlicht in: Nature Machine Intelligence, 2022, ISSN 2522-5839
Herausgeber: Nature Machine Intelligence
DOI: 10.48550/arXiv.2202.01338

Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection

Autoren: Jalencas, Xavier and Berg, Hannes and Espeland, Ludvik Olai and Sreeramulu, Sridhar and Kinnen, Franziska and Richter, Christian and Georgiou, Charis and Yadrykhinsky, Vladyslav and Specker, Edgar and Jaudzems, Kristaps and Miletić, Tanja and Harmel, Robe
Veröffentlicht in: RSC Medicinal Chemistry, 2024, ISSN 2632-8682
Herausgeber: RSC Medicinal Chemistry
DOI: 10.1039/D3MD00724C

The rise of automated curiosity-driven discoveries in chemistry

Autoren: Latimah Bustillo, Teodoro Laino, and Tiago Rodrigues
Veröffentlicht in: Chemical Science, 2023, ISSN 2041-6520
Herausgeber: Royal Society of Chemistry
DOI: 10.1039/D3SC03367H

Controlling the incorporation of fluorinated amino acids in human cells and its structural impact

Autoren: Azzurra Costantino, Lan B. T. Pham, Letizia Barbieri, Vito Calderone, Gili Ben-Nissan, Michal Sharon, Lucia Banci, Enrico Luchinat
Veröffentlicht in: Protein Science, 2024, ISSN 1572-3887
Herausgeber: Springer Verlag
DOI: 10.1002/PRO.4910

Biomacromolecules

Autoren: Fallarini S.; Cerofolini L.; Salobehaj M.; Rizzo D.; Gheorghita G. R.; Licciardi G.; Capialbi D. E.; Zullo V.; Sodini A.; Nativi C.; Fragai M.
Veröffentlicht in: Biomacromolecules, 2023, ISSN 1525-7797
Herausgeber: American Chemical Society
DOI: 10.1021/acs.biomac.3c00893

Combining Solid‐State NMR with Structural and Biophysical Techniques to Design Challenging Protein‐Drug Conjugates

Autoren: Linda Cerofolini, Kristian Vasa, Elisa Bianconi, Maria Salobehaj, Giulia Cappelli, Alice Bonciani, Giulia Licciardi, Anna Pérez‐Ràfols, Luis Padilla‐Cortés, Sabrina Antonacci, Domenico Rizzo, Enrico Ravera, Caterina Viglianisi, Vito Calderone, Giacomo Parigi, Claudio Luchinat, Antonio Macchiarulo, Stefano Menichetti, Marco Fragai
Veröffentlicht in: Angewandte Chemie International Edition, Ausgabe 62, 2023, ISSN 1433-7851
Herausgeber: Wiley
DOI: 10.1002/ANIE.202303202

Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins

Autoren: Lucia Gigli, José Malanho Silva, Linda Cerofolini, Anjos L. Macedo, Carlos F. G. C. Geraldes, Elizaveta A. Suturina, Vito Calderone, Marco Fragai, Giacomo Parigi, Enrico Ravera, Claudio Luchinat
Veröffentlicht in: Inorganic Chemistry, Ausgabe 63, 2024, ISSN 0020-1669
Herausgeber: American Chemical Society (ACS)
DOI: 10.1021/ACS.INORGCHEM.4C01274

EasyGrid: A versatile platform for automated cryo-EM sample preparation and quality control

Autoren: Olivier Gemin, Victor Armijo, Michael Hons, Caroline Bissardon, Romain Linares, View ORCID ProfileMatthew W. Bowler, Georg Wolff, View ORCID ProfileKirill Kovalev, Anastasiia Babenko, Veijo T. Salo, Sarah Schneider, Christopher Rossi, Léa Lecomte, Thiba
Veröffentlicht in: bioRXiv, 2024, ISSN 2692-8205
Herausgeber: bioRXiv
DOI: 10.1101/2024.01.18.576170

Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies

Autoren: Nadide Altincekic, Nathalie Jores, Frank Löhr, Christian Richter, Claus Ehrhardt, Marcel J. J. Blommers, Hannes Berg, Sare Öztürk, Santosh L. Gande, Verena Linhard, Julien Orts, Marie Jose Abi Saad, Matthias Bütikofer, Janina Kaderli, B. Göran Karlsson, U
Veröffentlicht in: ACS Chemical Biology, 2024, ISSN 1872-3136
Herausgeber: Bentham Science Publishers
DOI: 10.1021/ACSCHEMBIO.3C00720

eLife

Autoren: Isabelle Petit-Härtlein; Annelise Vermot; Michel Thépaut; Anne Sophie Humm; Florine Dupeux; Jérôme Dupuy; Vincent Chaptal; José A. Marquez; Susan M.E. Smith; Franck Fieschi
Veröffentlicht in: eLife, 2023, ISSN 2050-084X
Herausgeber: eLife Sciences Publications
DOI: 10.7554/ELIFE.93759

The future of integrated structural biology

Autoren: Harald Schwalbe, Pauline Audergon, Natalie Haley, Claudia Alen Amaro, Jon Agirre, Marc Baldus, Lucia Banci, Wolfgang Baumeister, Martin Blackledge, Jose Maria Carazo, Kristina Djinovic Carugo, Patrick Celie, Isabella Felli, Darren J. Hart, Thomas Hauß, Lari Lehtiö, Kresten Lindorff-Larsen, José Márquez, André Matagne, Roberta Pierattelli, Antonio Rosato, Frank Sobott, Sridhar Sreeramulu, Jan Steyaert, Joel L. Sussman, Lukas Trantirek, Manfred S. Weiss, Matthias Wilmanns
Veröffentlicht in: Structure, Ausgabe 32, 2025, ISSN 0969-2126
Herausgeber: Cell Press
DOI: 10.1016/J.STR.2024.08.014

NMR 1H,19F-based screening of the four stem-looped structure 5_SL1–SL4 located in the 5′-untranslated region of SARS-CoV 2 RNA

Autoren: Daniel Hymon, Jason Martins, Christian Richter, Sridhar Sreeramulu, Anna Wacker, Jan Ferner, Neeraj N. Patwardhan, Amanda E. Hargrove, and Harald Schwalbe
Veröffentlicht in: RSC Medicinal Chemistry, 2024, ISSN 2632-8682
Herausgeber: RSC Medicinal Chemistry
DOI: 10.1039/D3MD00322A