Non-globular proteins in the era of Machine Learning

COST Action CA21160


1st ML4NGP MEETING on Machine Learning and Non-globular proteins

July 5-7, 2023

Bratislava, Slovakia

Panoramic views of Bratislava, Slovakia (royalty free images).

welcome message

Non-globular proteins (NGPs) heterogeneous structural states and low sequence complexity challenge current experimental structure determination techniques and machine learning (ML) methods for structure prediction, making the molecular understanding of their sequence-structure-dynamics-function relationship difficult. The recent improvements of ML approaches and advances in determining NGP structural ensembles call for a timely re-assessment of the interplay between experiments and computation.

The 1st ML4NGP MEETING 2023 will be held from July 5 to 7 in Bratislava providing an opportunity for computational researchers and experimentalists interested in adapting Machine Learning tools and advancements for the study of NGPs to present and discuss current developments in the field.

This meeting is organized in the framework of COST ACTION CA21160 Non-globular proteins in the era of Machine Learning – ML4NGP, IDPFun (“Driving the functional characterization of intrinsically disordered proteins”) and REFRACT (“Repeat protein Function, Refinement, Annotation and Classification of Topologies”). It is hosted by the Institute of Neuroimmunology, Slovak Academy of Sciences.

The program includes a pre-event meeting on July 4, which is exclusive for ML4NGP Core Group members. 


Group photo with the participants and speakers of the first annual ML4NGP meeting held in Bratislava, Slovakia from 5 to 7 July 2023.

abstract information

Abstract submissions are no longer accepted. 

The abstract should be of maximum 400 words and have a brief and concise summary of the background/motivation for the study, method and result(s), as well as conclusion/statement of significance. The abstract is submitted through the submission form. Submitters may choose to have their submission consider for talk and poster or poster only. Those abstracts which are not selected for talk will be considered for a poster.

*A few poster abstracts will be selected to give a flash presentation during the symposium.

Location & venue

The 1st ML4NGP Meeting 2023 will take a place at the Clarion Congress Hotel Bratislava. 


Bratislava is a small historical city, but largest in Slovakia and a youngest european metropolis with many shopping, dining and natural wonders. Find more about our beautiful city at the official webpage:

Royalty free images


In Clarion Congress Hotel refined taste meets high functionality, modern interior with elegant use of space. Hotel offers unique, multifunctional conference rooms with modern technical equipment and variable configuration with elegant design for hosting international conferences.

It is easily accessible from Airport by public transport and within walking distance to downtown and all famous sights.

Clarion Congress Hotel****

Zabotova 2

811 04 Bratislava, Slovakia

Tel. +421 2 5727 7000


We would like to kindly suggest the Clarion Congress Hotel as the conference will be held in one of its conference halls. 

PRE-event meeting

Tuesday, July 4

16:00 – 18:00

Registration | Welcome desk

18:00 – 20:00

ML4NGP Core Group meeting | Closed session


Invited Speakers

Dr. Andrey KAJAVA

Centre de Recherche en Biologie cellulaire, Montpellier, France

Prof. Miguel ANDRADE

Johannes-Gutenberg University of Mainz, Mainz, Germany

Dr. Sonia LONGHI

CNRS and Aix-Marseille University, Marseille, France

Prof. Salvador VENTURA

Universitat Autònoma de Barcelona, Barcelona, Spain

Prof. Peter TOMPA

VIB-VUB Center for Structural Biology, Brussels, Belgium

Wednesday, July 5

08:00 – 09:00

Registration | Welcome desk

SESSION I - NGP classification

9:00 – 09:10

Opening Session

Alexander Monzon

9:10 – 09:40

Targeting disordered dipeptide repeats in ALS/FTD: a new modality in drug development

Peter Tompa

» Short Talks

9:40 – 10:00

Function of low complexity regions in literature: using transformer-based model to encode information in word embeddings
Sylwia Szymanska

10:00 – 10:20

Small-angle scattering for nonglobular proteins : perspectives of machine learning
Sergei Grudinin

10:20 – 10:40

Identifying novel short linear motifs based on a generalized machine-learning based bioinformatic pipeline
Matyas Pajkos

10:40 – 11:10

Coffee Break

SESSION II - Intrinsic Disorder

11:10 – 11:40

Intrinsic disorder and amyloid-like fibril formation by the Henipavirus V and W proteins

Sonia Longhi

» Short Talks

11:40 – 12:00

Mechanisms underlying functional selection in intrinsically disordered proteins
Lucia Beatriz Chemes

12:00 – 12:20

Decoding the Black Box of protein language models: A Basic Analysis of Sequence Features and Protein Disorder Encoding
Zsuzsanna Dosztányi

12:20 – 12:40

Detailed insight into dynamics of intrinsically disordered proteins using high-resolution relaxometry
Pavel Kadeřávek

12:40 – 14:00

Lunch Break

SESSION III - Machine Learning

14:00 – 14:30

Predicting Protein Aggregation: From Traditional Methods to Machine Learning

Andrey Kajava

» Short Talks

14:30 – 14:50

Defining and predicting conformational variability of proteins
Wim Vranken

14:50 – 15:10

A unified computational method with reinforcement learning for modeling conformational ensembles of complex protein architectures
Juan Cortes

15:10 – 15:30

Will the widespread use of AI-based structure prediction impact conformational ensemble use and ensemble generation?
Tamas Lazar

15:30 – 16:00

Coffee Break

SESSION IV - Protein Repeats

16:00 – 16:30

Evolutionary study of protein Short Tandem Repeats in protein families

Miguel Andrade

» Short Talks

16:30 – 16:50

Resolving the Fine Structure in the Energy Landscapes of Repeat Proteins
R. Gonzalo Parra

16:50 – 17:10

Trimeric Autotransporters: non-globular, repetitive virulence factors with peculiar genomic recombination mechanisms
Dirk Linke

17:10 – 17:30

Evolutionary splicing graphs for matching non-globular protein sequences and describing protein repeats alternative usage in evolution
Elodie Laine

18:30 – 20:00

Poster session and welcome reception

Thursday, July 6

08:00 – 09:00

Registration | Welcome desk

SESSION V - NGP aggregation

09:00 – 09:30

Structural determinants driving oligomer to fibril conversion in an amyloid disease

Salvador Ventura

» Short Talks

09:30 – 09:50

dGAE(297-391) tau fragment promotes formation of CTE-like full-length tau filaments
Kristaps Jaudzems

09:50 – 10:10

AmyloGraph: A comprehensive database of amyloid-amyloid interactions
Michal Burdukiewicz

10:10 – 10:30

Cryo-EM structure of hnRNPDL-2 fibrils, a functional amyloid associated with limb-girdle muscular dystrophy D3
Javier Garcia Pardo

10:30 – 11:00

Coffee Break

» Short Talks

11:00 – 11:20

Non-globular protein based biomaterials and therapeutics by design
Esra Yüca Yılmaz

11:20 – 11:40

Mapping the structural transitions of the flanking polyQ regions in huntingtin exon 1 upon membrane binding
Ana M. Melo

11:40 – 12:00

LEA4 proteins: How disordered are they?
Marija Vidovic

12:00 – 12:20

Energy Embedding Transformer Network: A Novel Approach to Predict Functional Disorder in Proteins
Gábor Erdős

12:20 – 14:00

Lunch Break

14:00 – 15:10

Flash Poster Presentations

» Short Talks

15:10 – 15:30

A systematic evaluation of AlphaFold-multimer for predicting LIR motif-Atg8 interactions
Vasilis Promponas

15:30 – 16:00

Coffee Break

16:00 – 17:15

WG1 meeting
hosted by Pavel Kadeřávek (WG1 leader)

17:15 – 17:45

WG5 meeting
hosted by Rita Vilaça (WG5 leader)

19:30 – 22:00

Social event and dinner at the “Hostinec U Deda” restaurant (website)

Friday, July 7

9:00 – 10:15

WG2 meeting
hosted by Zsuzsanna Dosztányi (WG2 leader)

10:15 – 10:45

Coffee Break

10:45 – 12:30

MC meeting

12:30  – 14:00


14:00 – 15:15

WG3 meeting
hosted by Jovana Kovačević (WG3 leader)

15:15 – 16:30

WG4 meeting
hosted by R. Gonzalo Parra (WG4 leader)



Alexander Monzon | Italy
Zuzana Bednarikova | Slovakia
Silvio Tosatto | Italy
Rita Vilaça | Portugal
Darius Sulskis | Lithuania
Pavel Kaderavek | Czech Republic
Zsuzsanna Dosztanyi | Hungary
Jovana Kovacevic | Serbia
Gonzalo Parra | Spain


Institute of Neuroimmunology SAS
Rostislav ŠKRABANA


contact information

Information and inquiry:



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


The presentations were very interesting and very helpful for my research in the future.

Testimonial #1 1st ML4NGP Meeting

Great program/speakers, adequate time for discussions/networking.

Testimonial #2 1st ML4NGP Meeting

Good balance between experimental/computational talks and the scientific networking.

Testimonial #3 1st ML4NGP Meeting

I really enjoy the breaks, poster session and dinner because that's when you get to know your colleagues and discuss about their current work and future perspectives.

Testimonial #4 1st ML4NGP Meeting