Non-globular proteins in the era of Machine Learning

COST Action CA21160

ML4NGP WORKSHOP

THIS EVENT HAS PASSED.

Resources and infrastructure to explore the continuum between globular and non-globular proteins

March 18-19, 2025

Barcelona, Spain

DESCRIPTION

The workshop was strategically scheduled just before the start of the Elixir 3DBioinfo 2025 meeting, providing an excellent opportunity to discuss the challenges and opportunities in exploring the continuum between globular and non-globular proteins, including IDPs, tandem repeat proteins, protein aggregation, and more. Our goal was to identify commonalities and foster synergies among key resources and databases such as CATH, TED, PDBeKB, PFAM/InterPro, MobiDB, PED, DisProt, Aggrescan4D and RepeatsDB.

The workshop also served as a platform to discuss examples provided by ML4NGP members in which AlphaFold predicts biologically incorrect models. The short-term goal for this initiative was to gather relevant information that will used to produce a community paper to caution scientists against blindly accepting AlphaFold results without critical evaluation.

Participants

Gonzalo Parra, Barcelona Supercomputing Center, Spain
Alexander Monzon, University of Padova, Italy
Silvio Tosatto, University of Padova, Italy
Maria Cristina Aspromonte, University of Padova, Italy
Christine Orengo, University College London, UK
Nicola Bordin, University College London, UK
Gabor Erdos, Eötvös Loránd University, Hungary
Salvador Ventura, Autonomous University of Barcelona, Spain
Javier Garcia-Pardo, Autonomous University of Barcelona, Spain
Typhaine Paysan-Lafosse, European Bioinformatics Institute, UK
Jennifer Fleming, European Bioinformatics Institute, UK
Juan Cortes, LAAS-CNRS, France
Miguel Andrade, Johannes Gutenberg University, Germany
Zarifa Osmanli, University of Padova, Italy
Sofia Duarte, Universidad Nacional del Litoral, Argentina
Khalil Joron, Hebrew University of Jerusalem, Israel
Pablo Mier, Universidad Pablo de Olavide, Spain
San Hadži, University of Ljubljana, Slovenia
Isabella Felli, CERM, University of Florence, Italy
Oriol Barcenas, Autonomous University of Barcelona, Spain
Rafayel Petrosyan, American University of Armenia, Armenia
Viktor Bartošík, Masaryk University, Czech Republic
Gavin Farrell, University of Padova, Italy
Pavel Kadeřávek, Masaryk University, Czech Republic
Miguel Romero, Barcelona Supercomputing Center, Spain
Tamas Hegedus, Institute of Biophysics and Radiation Biology, Semmelweis University, Hungary
Marija Vidović, Institute of Molecular Genetics and Genetic Engineering, Serbia
Simone Attanasio, Université libre de Bruxelles, Belgium

PRELIMINARY PROGRAM

MARCH 18, 2025

9:00 – 9:15	Registration & Welcome desk Sign the COST Action attendance sheet
9:15 – 9:30	Welcome note and goals – Alexander Monzon/Dirk Linke
Session 1: AlphaFold “failing” examples (Chair: Alexander Monzon)
9:30 – 11:00	Present your submitted example in 5 minutes: What are the biological reasons behind this example of “failure”? Focus on discussing structural/functional/evolutionary aspects. Gabor Erdos Juan Cortes Miguel Andrade Pablo Mier Pavel Kadeřávek / Viktor Bartošík Khalil Joron San Hadži Isabella Felli Salvador Ventura / Oriol Barcenas Lopez Rafayel Petrosyan Tamas Hegedus Marija Vedovic Questions and Discussion
11:00 – 11:30	Coffee break
11:30 – 13:00	Defining Action Items and responsibilities to write a community paper
13:00 – 15:00	Lunch break
Session 2: DBs synergies – Part I (Chair: Silvio Tosatto)
15:00 – 16:00	Short talks (15 min): Provide an overview of key features and data of each resource. The Encyclopedia of Domains (TED) – Nicola Bordin CATH database – Christine Orengo RepeatsDB – Zarifa Osmanli InterPro/PFAM – Typhaine Paysan-Lafosse Q&A
16:00 – 16:30	Coffee break
16:30 – 18:00	Open discussion about synergies Manage of non-globular regions Data sharing Cross Linking Sustainability

MARCH 19, 2025

Session 3: DBs synergies – Part II (Chair: Gonzalo Parra)
9:30 – 10:30	Short talks (15 min): Provide an overview of key features and data of each resource. Aggrescan4D – Salvador Ventura MobiDB/Protein Ensemble Database (PED) – Alexander Monzon DisProt database – Maria Cristina Aspromonte PDBe-KB and AlphaFoldDB – Jennifer Fleming Q&A
10:30 – 11:00	Coffee break
11:00 – 12:00	Final Discussion and Future Activities

Location & venue

VENUE

Barcelona Supercomputing Center (Sala 1-3-2)

Plaça d’Eusebi Güell, 1-3, Les Corts, 08034 Barcelona

ORGANIZATION

Scientific COMMITTEE

Gonzalo Parra, Barcelona Supercomputing Center, Spain

Alexander Monzon, University of Padova, Spain
Silvio Tosatto, University of Padova, Spain

This event is part of the activities of the COST Action ML4NGP, CA21160, supported by COST (European Cooperation in Science and Technology).