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

Informazioni relative al progetto

Fragment-Screen

ID dell’accordo di sovvenzione: 101094131

DOI

10.3030/101094131

Data della firma CE 13 Dicembre 2022

Data di avvio 1 Febbraio 2023

Data di completamento 31 Gennaio 2026

Finanziato da

• Research infrastructures

Costo totale

€ 8 265 079,64

Contributo UE

€ 8 265 079,64

Coordinato da

INSTRUCT-ERIC
United Kingdom

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 (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

Pubblicazioni

Book chapters (1)

Language Models in Molecular Discovery

Autori: Nikita Janakarajan, Tim Erdmann, Sarath Swaminathan, Teodoro Laino, Jannis Born
Pubblicato in: Drug Development Supported by Informatics, 2024
Editore: 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

Autori: Jannis Born, Matteo Manica
Pubblicato in: Nature Machine Intelligence, 2022, ISSN 2522-5839
Editore: 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

Autori: 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
Pubblicato in: RSC Medicinal Chemistry, 2024, ISSN 2632-8682
Editore: RSC Medicinal Chemistry
DOI: 10.1039/D3MD00724C

The rise of automated curiosity-driven discoveries in chemistry

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

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

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

Biomacromolecules

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

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

Autori: 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
Pubblicato in: Angewandte Chemie International Edition, Numero 62, 2023, ISSN 1433-7851
Editore: Wiley
DOI: 10.1002/ANIE.202303202

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

Autori: 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
Pubblicato in: Inorganic Chemistry, Numero 63, 2024, ISSN 0020-1669
Editore: American Chemical Society (ACS)
DOI: 10.1021/ACS.INORGCHEM.4C01274

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

Autori: 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
Pubblicato in: bioRXiv, 2024, ISSN 2692-8205
Editore: bioRXiv
DOI: 10.1101/2024.01.18.576170

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

Autori: 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
Pubblicato in: ACS Chemical Biology, 2024, ISSN 1872-3136
Editore: Bentham Science Publishers
DOI: 10.1021/ACSCHEMBIO.3C00720

eLife

Autori: 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
Pubblicato in: eLife, 2023, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/ELIFE.93759

The future of integrated structural biology

Autori: 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
Pubblicato in: Structure, Numero 32, 2025, ISSN 0969-2126
Editore: 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

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