Non-globular proteins in the era of Machine Learning
COST Action CA21160
2nd ML4NGP-REFRACT WORKSHOP
Workshop on computational methods for tandem repeat proteins
September 26-28, 2023
Montpellier, France
DESCRIPTION
The purpose of this workshop is to cover the state-of-the-art methods and techniques for identifying and characterizing tandem repeat proteins (TRPs), and to explore how the new structural data from AlphaFold models can contribute to this endeavor. The workshop is targeted at young researchers (PhD students, post-docs, and young researchers) and principal investigators who are interested in this topic. The workshop will be co-organized with the MSCA RISE consortium REFRACT which aims to extend our knowledge of the mechanism of tandem repeat protein (TRP) function and evolution, establishing a common classification and best practices.
THIS EVENT HAS ENDED.
PROGRAM
SEPTEMBER 26, 2023
Location: IGMM building – CNRS, Montpellier
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9:00 – 9:30 |
Registration & Welcome desk Sign the COST Action attendance sheet |
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Session 1 (Chair: Silvio Tosatto) |
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9:30 – 9:40 |
Welcome – Andrey Kajava |
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9:40 – 11:00 |
“A STRP-ed definition of Structured Tandem Repeats in Proteins” Alexander Monzon (25’ + 5’ Q&A)
“The shape of flower” Antonina Andreeva – (25’ + 5’ Q&A)
”T-REx. A Tandem Repeat Explorer algorithm for the fast, accurate and simple detection of tandem repeated proteins based on their secondary structures” David Moyano – (15’ + 5’ Q&A) |
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11:00 – 11:40 |
Coffee break |
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11:40 – 12:50 |
”Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space” Daniel Ridgen – (25’ + 5’ Q&A)
“Cross-Beta DB & Cross-Beta RF Predictor: 2 upcoming tools for analyzing and predicting amyloids” Valentin Gonay – (15’ + 5’ Q&A)
“Sequence, Structure, Energetic and Dynamic Characterization of the Ankyrin Repeat Protein Family” Gonzalo Parra – (15’ + 5’ Q&A) |
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13:00 – 14:30 |
Lunch break |
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Session 2: Future of RepeatsDB (Chair:Andrey Kajava) |
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14:30 – 16:00 |
“RepeatsDB in 2024” Damiano Clementel – (25’ + 5’ Q&A)
Round table discussion |
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16:00 – 16:30 |
Coffee break |
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16:30 – 17:20 |
”Tandem repeat adhesins and dead repeat genes in bacteria” Dirk Linke – (25’ + 5’ Q&A)
“Reconciling diversity of substrate binding mechanisms within the highly conserved KELCH repeat proteins” Matyas Pajkos – (15’ + 5’ Q&A) |
SEPTEMBER 27, 2023
Location: IGMM building – CNRS, Montpellier
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Session 3: (Chair: TBA) |
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9:30 – 9:35 |
Recap of first day |
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9:35 – 10:55 |
“New pipelines and tools for discoveries in protein structure space” Nicola Bordin – (25’ + 5’ Q&A)
“Membrane coat proteins in Bacteria: an update” Damien Devos – (25’ + 5’ Q&A)
”Novel approach in predicting Structured Tandem Repeats in Proteins (STRPs)” Sourush Mozaffari – (15’ + 5’ Q&A) |
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11:00 – 11:30 |
Coffee break |
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11:30 – 13:00 |
“Structure/function relationship in homorepeats” Pau Bernado – (25’ + 5’ Q&A)
”Prediction of the function of protein interactions in post-translational modifications” Aimilia Vagiona – (15’ + 5’ Q&A)
“Tandem repeat proteins from ML perspective” Jovana Kovacevic – (15’ + 5’ Q&A)
“Structure variability of AlphaFold models across protein families” Francesco Costa – (15’ + 5’ Q&A) |
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13:00 – 14:30 |
Lunch break |
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Session 4: Repeat classification and future directions (Chair: TBA) |
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14:30 – 16:00 |
Andrey Kajava’s classification (25’ + 5’ Q&A) Round table discussion |
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16:00 – 16:30 |
Coffee break |
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16:30 – 17:30 |
Repeat community discussion Fundraising and grant opportunities |
SEPTEMBER 28, 2023
Location: IGMM building – CNRS, Montpellier
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Session 5: (Chair:TBA) |
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9:30 – 9:35 |
Recap of second day |
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09:35 – 11:00 |
“Why does the first protein repeat often become the only one?” Andrey Kajava -(25’ + 5’ Q&A)
“Systematic investigation of the sequence context in Arginine/Glycine-Rich Proteins through feature-function correlation” Eric Schumbera – (15’ + 5’ Q&A)
“Exploring tandem repeats in the alternative proteomes” Zarifa Osmanli – (15’ + 5’ Q&A)
“Unraveling the Contributions of Three Distinct Paths of Protein Evolution across the Tree of Life” Ruben García Domínguez – (15’ + 5’ Q&A) |
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11:00 – 11:30 |
Coffee break |
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11:30 – 13:00 |
Final Discussion and Action Items |
Location & venue
The 2nd ML4NGP workshop will take place in Montpellier, France.
VENUE
French National Centre for Scientific Research – Centre for Biochemical and Macromolecular Research
1919 Rte de Mende, 34090 Montpellier, France
+33 4 34 35 94 00
ORGANIZATION
Scientific COMMITTEE
Andrey Kajava, Centre National de la Recherche Scientifique (CNRS), France
Alexander Monzon, Department of Information Engineering, University of Padova, Italy
Silvio Tosatto, Department of Biomedical Sciences, University of Padova, Italy
LOCAL ORGANIZING COMMITTEE
Andrey Kajava, Centre National de la Recherche Scientifique (CNRS), France
Gudrun Aldrian, Centre National de la Recherche Scientifique (CNRS), France
This event is part of the activities of the COST Action ML4NGP, CA21160, supported by COST (European Cooperation in Science and Technology).