After the success of the 2020 Remote Summer School, BioExcel is organising a winter edition of the course.
Date: Monday 30 November – Friday 4 December 2020
Venue: Remote
Application deadline: 18 October 2020
Notification date: 28 October 2020
Participation: Open application with selection
Registration fee: 50 Euros (to be paid after the selection process)
Contact: Michelle Mendonca
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.
– Applications are now closed –
- Molecular Dynamics simulations
- Biomolecular Docking
- Free energy calculations
- Advanced sampling methods (Metadynamics)
- BioExcel Building Blocks (BioBB)
- 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)
- You have the pre-requisite knowledge
- Your research and your research group will 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
Time (CET) | Topic | Format | Trainer |
Day 1 - Monday 30 November | |||
09:00 - 09:20 | Course introduction | Live | Marta Lloret Llinares, Alexandre Bonvin |
09:20 - 09:40 | BioExcel introduction | Live | Rossen Apostolov |
09:40 - 10:20 | Participant presentations | Live | |
10:20 - 10:50 | Virtual coffee & tea break | ||
10:50 - 11:40 | Docking basics | Pre-recorded lecture 1 | Alexandre Bonvin |
11:40 - 12:30 | Docking basics | Pre-recorded lecture 2 | Alexandre Bonvin |
12:30 - 12:55 | Q&A | Live | Alexandre Bonvin |
12:55 - 14:00 | Break | ||
14:00 - 14:40 | Participant presentations | Live | |
14:50 - 16:50 | Tutorial - HADDOCK | Work on your own with live support | Alexandre Bonvin, Zuzana Jandova |
Time (CET) | Topic | Format | Trainer |
Day 2 - Tuesday 1 December | |||
09:00 - 09:30 | Basis of molecular dynamics simulations | Pre-recorded lecture 1 | Alessandra Villa |
09:30 - 10:05 | Basis of molecular dynamics simulations | Pre-recorded lecture 2 | Alessandra Villa |
10:05 - 10:30 | Q&A | Live | Alessandra Villa |
10:30 - 11:00 | Virtual coffee & tea break | ||
11:00 - 12:30 | Tutorial - A guide to perform MD simulation with GROMACS | Live | Christian Blau, Alessandra Villa & Artem Zhmorov |
12:30 - 13:30 | Break | ||
13:30 - 14:20 | BioExcel building blocks (BioBB) | Pre-recorded lecture | Adam Hospital |
14:20 - 15:00 | Computational biomolecular simulation workflows using BioBB | Pre-recorded lecture | Adam Hospital |
15:00 - 15:25 | Q&A | Live | Adam Hospital |
15:30 - 16:30 | Course social event |
Time (CET) | Topic | Format | Trainer |
Day 3 - Wednesday 2 December | |||
09:00 - 09:30 | Introduction to QM/MM | Pre-recorded lecture 1 | Emiliano Ippoliti |
09:30 - 10:10 | Introduction to QM/MM | Pre-recorded lecture 2 | Emiliano Ippoliti |
10:10 - 10:35 | Q&A | Live | Emiliano Ippoliti |
10:40 - 11:10 | Virtual coffee & tea break | ||
11:10 - 12:40 | Tutorial - Introduction to QM/MM simulations: GROMACS-CP2K Interface | Live | Dmitry Morozov Vaibhav Modi |
12:40 - 13:40 | Break | ||
13:40 - 15:10 | Tutorial - Protein-Complex MD Setup with Jupyter Notebooks and BioBB | Live | Adam Hospital |
15:15 - 17:00 | Poster session |
Time (CET) | Topic | Format | Trainer |
Day 4 - Thursday 3 December | |||
09:00 - 10:00 | Modeling molecular recognition through enhanced-sampling methods | Pre-recorded lecture 1 | Attilio Vargiu |
10:00 - 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 - 14:50 | Cryo-EM densities vs. Stereochemistry | Christian Blau | |
14:50 - 15:10 | Q&A | Live | |
15:10 - 16:10 | Round table about career options | Rosa M. Badia, Piraveen Gopalasingam, Richard Norman | |
16:10 - 17:00 | Poster and Networking session |
Time (CEST) | Topic | Format | Trainer |
Day 5 - Friday 4 December | |||
09:00 - 09:50 | 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 | When HADDOCK meets GROMACS | Zuzana Jandova | |
14:50 - 15:10 | Q&A | Live | |
15:10 - 15:30 | Using GROMACS and pmx with the BioExcel Building Blocks (BioBB) library to tackle COVID-19 research | Adam Hospital | |
15:30 - 15:50 | Q&A | Live | |
15:50 - 16:20 | 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
Organisers
- 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