Non-globular proteins in the era of Machine Learning
COST Action CA21160
1ST ML4NGP TRAINING SCHOOL
THIS EVENT HAS PASSED.
Protein aggregation, intrinsic disorder and phase separation in the era of machine learning
April 19-21 2023
Porto, Portugal
DESCRIPTION
The COST Action ML4NGP is pleased to announce its 1st Training School on “Protein aggregation, intrinsic disorder and phase separation in the era of machine learning”. The event was co-organized with the H2020-funded Twinning project PhasAGE (GA 952334) and the H2020-MSCA-RISE project IDPFun (GA 778247), and took place at the i3S, in Porto (Portugal), from 19 to 21 April 2023.
The 1st ML4NGP Training School was organized in parallel with the PhasAGE Training School and IDPfun Training School with shared theoretical lectures and computational practical sessions.
The main goal of this training school was to provide participants with an overview of recent advances in computational resources and hands-on training with resources and tools for studying protein aggregation and phase separation. Participants were challenged to reflect on how recent advances in protein structure ML prediction tools are paving the way for a more comprehensive understanding of protein function.
The scientific program included lectures and practical sessions. A dinner and social event was also organized for participants.
The program also included a career development workshop on alternative career paths in biophysics and computational structural biology to help early-stage researchers maximize their professional potential.
TARGET AUDIENCE AND REQUIREMENTS
Exclusive for working group members. Participants were selected by the organizing committee in order to guarantee gender balance, early career researchers (PhD students and Junior postdocs) and geographic distribution. The Training School was limited to a reduced number of attendees to maximize active learning.
This Training school was intended for those who are interested in learning how to better predict and correlate protein structure and function. Participants were expected to navigate online biological resources but were not expected to have computational or programming skills. Prior knowledge and basic training in Biochemistry, Biology, Bioengineering or related sciences were recommended.
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Meal fee |
Application Deadline |
Payment Deadline |
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ML4NGP WG members |
70 EUR |
March 9, 2023 |
March 17, 2023 |
Meal package fee includes coffee breaks, lunches and access to the social event and course dinner on 19 April.
Please note that your application does not confirm that you have been selected for the course. You will be informed before the early registration deadline. Payment will be requested only after confirmation of acceptance. Details for payment will be sent in the confirmation registration e-mail
- A short motivation statement (max. 500 characters) and CV will be requested in the application form
- COST Action ML4NGP can reimburse travel expenses for a maximum of 15 participants
- Participants should bring their own laptop
- A certificate of attendance will be sent no later then one week after the end of the school
FINAL PROGRAM
19 APRIL 2023
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09:00-10:00 |
AI revolution and protein structure models |
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10:00-11:15 |
PhasAGE-ML4NGP-IDPfun Computational Session – part I |
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11:15-11:30 |
Coffee Break |
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11:30-12:45 |
PhasAGE-ML4NGP-IDPfun Computational Session – part II |
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12:45-14:00 |
Lunch |
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14:00-15:30 |
Mathematical models and data analysis |
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15:30-16:00 |
Modulators of Ataxin-3 protein aggregation Sandra Ribeiro |
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16:00-16:15 |
Coffee Break |
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16:15-17:15 |
Career Development Talk |
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17.30-22:00 |
Social event and Dinner |
20 APRIL 2023
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10:00-11:00 |
The structure-toxicity relationship of protein aggregates |
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11:00-11:15 |
Coffee Break |
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11:15-12:15 |
Conformational ensembles of IDPs: implications for function and drug development |
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12:15-13:00 |
iPLUS: on the function of a non-coding sequence as an asset for biopharmaceutics Alexandra Moreira |
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13:00-14:30 |
Lunch |
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14:30-16:00 |
ML4NGP-IDPfun Practical Session |
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16:00-16:15 |
Coffee Break |
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16:15-17:45 |
ML4NGP-IDPfun Practical Session |
21 APRIL 2023
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9:30-10:30 |
NMR as a tool to study disordered proteins at atomic resolution |
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10:30-10:45 |
Coffee Break |
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10:45-11:45 |
CAID 2: lessons from the second critical assessment of protein intrinsic disorder prediction |
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12:00-13:00 |
Disordered interactions and phase separations of α-synuclein |
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13:00-14:30 |
Lunch |
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14:30-16:00 |
Trainees presentations & closing remarks |
Practical Sessions
Introduction to Machine Learning Methods in Biology | Jovana Kovačević
In this practical session, participants will be introduced to the basic concepts and techniques of machine learning and their applications in biology with a special emphasis to non-globular proteins. The session will begin with an overview of machine learning and will focus mainly on supervised learning methods. Participants will then learn how to use popular machine learning tools and libraries, such as Pandas, to analyze biological datasets. They will work through several hands-on examples, including protein disorder prediction and disease classification using genomic data.
Local Energetic Frustration, Protein Function and Dynamics | Gonzalo Parra
In this practical session, participants will be introduced to the concept of local energetic frustration, derived from the energy landscapes theory for protein folding. The participants will get familiar with how to use local energetic frustration to understand energetic constraints in protein structures both at single instances and in the context of protein families. We will discuss the algorithms to calculate frustration as well as how to interpret results in terms of protein stability and function. The application of these concepts to IDPs and repeat proteins will be discussed.
ORGANIZATION
SCIENTIFIC organizing COMMITTEE
Rita Vilaça (IBMC/i3S, University of Porto, Portugal)
Mónica Marques (IBMC/i3S, University of Porto, Portugal)
Sandra Ribeiro (IBMC/i3S, University of Porto, Portugal)
Alexander Monzon (University of Padova, Italy)
Silvio Tosatto (University of Padova, Italy)
CONSORTIA
This event is part of the activities of the COST Action ML4NGP, CA21160, supported by COST (European Cooperation in Science and Technology).