Date: 4 June (Introduction) and 7 – 11 June 2021
Venue: Remote
Application deadline: 11 April
Notification date: 27 April
Participation: Open application with selection
Registration fee: 50 Euros (to be paid after the selection process)
Contact: Michelle Mendonca
We highly encourage applications from women and underrepresented groups.
We recognise that participants may occasionally be unable to meet their financial obligations to us for registration fees. If you have been selected for the course and are experiencing financial hardship, problems with obtaining funding, or unsure about how you will pay for fees please talk to us. You can contact Michelle Mendonca at mmendonca@ebi.ac.uk.
- Molecular Dynamics simulations
- Biomolecular Docking
- Free energy calculations
- Advanced sampling methods (Metadynamics)
- BioExcel Building Blocks (BioBB)
- Quantum mechanics/molecular mechanics (QM/MM)
Audience and Prerequisites
The summer school is intended for researchers (primarily PhD and post-docs) using or planning to use biomolecular modeling and simulation in their everyday research. Familiarity with Linux and basic knowledge of molecular modelling software is a requirement.
- Support letter from your supervisor or a senior co-worker explaining why you should be selected for this course
- Research Abstract (limit: 250 words – you will be able to present and discuss your research during the course)
Once you have these ready, please complete the application process by midnight (BST) on Sunday 11 April. Incomplete applications will not be considered. All applicants will be informed of the status of their application (successful, waiting list, rejected) by Tuesday 27 April. If you have any questions regarding the application process, please contact Michelle Mendonca.
Tips for a good application
1) During the selection process we focus on:
- Do you have the pre-requisite knowledge?
- Will your research and research group benefit from what you learn in this course?
- Describe your research interests
- Describe how this course will benefit your own research
- Describe how this course will benefit the research of your group
This course is designed to ensure full-time participation with flexibility for time zones differences and childcare requirements. This can be discussed with the course coordinator prior to the course to formalise alternative arrangements. We are also organising a career session on Day 4 of the course featuring talks and networking opportunities with professionals from academia and industry.
Note: The programme is subject to minor changes
Time (CEST) | Topic | Format | Trainer |
Introduction - Friday 4 June | |||
13:00 - 13:20 | Course introduction | Live | Marta Lloret Llinares and Alexandre Bonvin |
13:20 - 13:40 | BioExcel introduction | Live | Rossen Apostolov |
13:40 - 15:30 | Participant presentations (in blocks of 20 mins with breaks of 10 mins in between) | Live |
Time (CEST) | Topic | Format | Trainer |
Day 1 - Monday 7 June | |||
09:00 - 09:40 | Docking basics | Pre-recorded lecture 1 | Alexandre Bonvin |
09:50 - 10:30 | Docking basics | Pre-recorded lecture 2 | Alexandre Bonvin |
10:30 - 10:55 | Q&A | Live | Alexandre Bonvin |
11:00 - 11:30 | Virtual Coffee and Tea Break | ||
11:30 - 13:30 | Tutorial - HADDOCK | Live support | Alexandre Bonvin, Zuzana Jandova |
13:30 - 14:30 | Break | ||
14:30 - 15:10 | BioExcel building blocks (BioBB) | Pre-recorded lecture | Adam Hospital |
15:20 - 16:00 | Computational biomolecular simulation workflows using BioBB | Pre-recorded lecture | Adam Hospital |
16:10 - 17:00 | Course social event |
Time (CEST) | Topic | Format | Trainer |
Day 2 - Tuesday 8 June | |||
09:00 - 09:40 | Basis of molecular dynamics simulations | Pre-recorded lecture 1 | Alessandra Villa |
09:50 - 10:30 | Basis of molecular dynamics simulations | Pre-recorded lecture 2 | Alessandra Villa |
10:30 - 10:55 | Q&A | Live | Alessandra Villa |
11:00 - 11:30 | Virtual coffee & tea break | ||
11:30 - 13:00 | Tutorial - A guide to perform MD simulation with GROMACS | Live | Christian Blau, Alessandra Villa & Artem Zhmorov |
13:00 - 14:00 | Break | ||
14:00 - 16:00 | Tutorial - Protein-Complex MD Setup with Jupyter Notebooks and BioBB Includes Q&A for BioBB lectures | Live | Adam Hospital |
Time (CEST) | Topic | Format | Trainer |
Day 3 - Wednesday 9 June | |||
09:00 - 09:40 | Introduction to QM/MM | Pre-recorded lecture 1 | Emiliano Ippoliti |
09:50 - 10:30 | Introduction to QM/MM | Pre-recorded lecture 2 | Emiliano Ippoliti |
10:30 - 10:55 | Q&A | Live | Emiliano Ippoliti |
11:00 - 11:30 | Virtual coffee & tea break | ||
11:30 - 13:30 | Tutorial - Introduction to QM/MM simulations | Live | Dmitry Morozov |
13:30 - 14:30 | Break | ||
14:30 - 14:50 | Short talk #1 | Pre-recorded lecture | |
14:50 - 15:10 | Q&A | Live | |
15:20 - 17:00 | Poster session |
Time (CEST) | Topic | Format | Trainer |
Day 4 - Thursday 10 June | |||
09:00 - 09:40 | Modeling molecular recognition through enhanced-sampling methods | Pre-recorded lecture 1 | Attilio Vargiu |
09:50 - 10:30 | Modeling molecular recognition through enhanced-sampling methods | Pre-recorded lecture 2 | Attilio Vargiu |
10:30 - 10:55 | Q&A | Live | Attilio Vargiu, Giuliano Malloci & Andrea Basciu |
11:00 - 11:30 | Virtual coffee & tea break | ||
11:30 - 13:30 | Metadynamics tutorial - Guided introduction | Work on your own with live support | Andrea Basciu, Giuliano Malloci & Attilio Vargiu |
13:30 - 14:30 | Break | ||
14:30 - 15:30 | Round table about career options | Live | |
15:40 - 17:00 | Poster & networking session | Live |
Time (CEST) | Topic | Format | Trainer |
Day 5 - Friday 11 June | |||
09:00 - 09:40 | Introduction to free energy calculations | Pre-recorded lecture | Bert de Groot |
09:50 - 10:30 | Applications of alchemical free energy calculations | Pre-recorded lecture | Vytautas Gapsys |
10:30 - 10:55 | Q&A | Live | Bert de Groot & Vytautas Gapsys |
11:00 - 11:30 | Virtual coffee & tea break | ||
11:30 - 13:30 | Tutorial - PMX | Live | Bert de Groot & Vytautas Gapsys |
13:30 - 14:30 | Break | ||
14:30 - 14:50 | Short talk #2 | Pre-recorded lecture | |
14:50 - 15:10 | Short talk #3 | Pre-recorded lecture | |
15:10 - 15:40 | Q&A | ||
15:40 - 16:10 | Final questions, remarks and feedback | Live |
The lectures and hands-on sessions will be given by internationally recognised leaders in the field of computational biomolecular research.
Speakers
- Alexandre Bonvin, BioExcel (University of Utrecht)
- Alessandra Villa, BioExcel (KTH)
- Christian Blau, BioExcel (KTH)
- Adam Hospital, BioExcel (IRB Barcelona)
- Emiliano Ippoliti, BioExcel (FZ Jülich)
- Bert de Groot, BioExcel (Max Planck Institute)
- Vytautas Gapsys, BioExcel (Max Planck Institute)
- Giuliano Malloci, University of Cagliari
- Attilio Vittorio Vargiu, University of Cagliari
- Vera Matser, BioExcel (EMBL-EBI)
- Marta Lloret Llinares, BioExcel (EMBL-EBI)
- Alexandre Bonvin, BioExcel (University of Utrecht)
- Attilio Vittorio Vargiu, University of Cagliari
- Giuliano Malloci, University of Cagliari
Date/Time
04 Jun, 2021 - 11 Jun, 2021
10:00 - 18:00
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