Due to the current coronavirus pandemic, BioExcel has taken the decision to convert the face-to-face into a remote BioExcel Summer School with a limited programme.
We aim to open our lectures to all applicants, while introducing the selection process only for the live hands-on practicals. Although the programme is set to Central European Summer Time, we will provide alternative support options if the selected participant is unable to join a live session. For all applicants who have not been selected, a notification will be sent out of when the pre-recorded lectures will be made available on the website.
– The programme is subject to minor changes –
Programme
| Time (CEST) | Topic | Format | Trainer / Speaker |
| Day 1 – Monday 22 June 2020 | |||
| 09:00 – 09:20 |
Course introduction |
Live |
Marta Lloret Llinares & Alexandre Bonvin |
| 09:20 – 09:40 |
BioExcel introduction |
Live |
Rossen Apostolov |
| 09:40 – 10:30 | Participant introductions | Live | |
| 10:30 – 11:00 | Coffee & tea break | ||
| 11:00 – 11:45 | Docking basics | Pre-recorded lecture 1 | Alexandre Bonvin |
| 11:45 – 12:25 | Docking basics | Pre-recorded lecture 2 | Alexandre Bonvin |
| 12:25 – 12:45 | Q&A session | Live | Alexandre Bonvin |
| 12:45 – 13:45 | Break | ||
| 13:45 – 15:45 |
Tutorial: HADDOCK; |
Live |
Alexandre Bonvin & Zuzana Jandova |
| Day 2 – Tuesday 23 June 2020 | |||
| 09:00 – 09:30 | Basics of molecular dynamics simulations | Pre-recorded lecture 1 | Alessandra Villa |
| 09:35 – 10:05 | Basics of molecular dynamics simulations | Pre-recorded lecture 2 | Alessandra Villa |
| 10:05 – 10:30 | Q&A session | Live | Alessandra Villa |
| 10:30 – 11:00 | Coffee & tea break | ||
| 11:00 – 12:30 | Tutorial – A guide to perform MD simulation with GROMACS | Live | Christian Blau, Alessandra Villa & Paul Bauer |
| 12:30 – 13:30 | Break | ||
| 13:30 – 14:10 | BioExcel building blocks (BioBB) | Pre-recorded lecture | Adam Hospital |
| 14:15 – 14:45 | Computational biomolecular simulation workflows using BioBB | Pre-recorded lecture | Adam Hospital |
| 14:45 – 15:05 | Q&A session | Live | Adam Hospital, Genís Bayarri & Pau Andrio |
| 15:05 – 15:30 | Break |
||
| 15:30 – 17:00 | Tutorial: Protein-Complex MD Setup with Jupyter Notebooks and BioBB | Live | Adam Hospital, Genís Bayarri & Pau Andrio |
| Day 3 – Wednesday 24 June 2020 | |||
| 09:00 – 09:40 |
Modeling molecular recognition through enhanced-sampling methods | Pre-recorded lecture 1 | Attilio Vargiu |
| 09:40 – 10:10 | Modeling molecular recognition through enhanced-sampling methods | Pre-recorded lecture 2 | Attilio Vargiu |
|
10:10 – 10:30 |
Q&A session |
Live | Attilio Vargiu, Giuliano Malloci & Andrea Basciu |
|
10:30 – 11:00 |
Coffee & tea break |
||
| 11:00 – 12:30 | Tutorial: Metadynamics – guided intro; Work on your own with live support and Q/A | Live | Andrea Basciu, Giuliano Malloci & Attilio Vargiu |
| 13:00 – 14:00 | Lunch Break | ||
| 14:00 – 14:40 | GROMACS features and future | Pre-recorded lecture 1 | Paul Bauer |
| 14:40 – 15:00 | Q&A session | Live | Paul Bauer |
| 15:00 – 15:30 |
Coffee and tea break |
||
| 15:30 – 16:30 | Poster session |
||
| Day 4 – Thursday 25 June 2020 | |||
| 09:00 – 09:40 | Introduction to QM/MM | Pre-recorded lecture 1 | Emiliano Ippoliti |
| 09:40 – 10:10 | Introduction to QM/MM | Pre-recorded lecture 2 | Emiliano Ippoliti |
| 10:10 – 10:30 | Q&A session | Live | Emiliano Ippoliti & Vaibhav Modi |
| 10:30 – 11:00 | Coffee and tea break | ||
| 11:00 – 13:00 | Tutorial: CP2K | Live | Vaibhav Modi |
| 13:00 – 14:00 | Break | ||
| 14:00 – 14:40 | Q&A session: CP2K | Live | Emiliano Ippoliti & Vaibhav Modi |
| 14:40 – 15:00 | Moving mutational analysis into the structural field for drug design: changes in ligand binding affinities upon protein residue mutations in the EGFR kinase domain | Pre-recorded lecture | Francesco Colizzi |
| 15:00 – 15:20 | Q&A session | Live | |
| 15:20 – 15:50 | Coffee and tea break |
||
| 15:50 – 16:10 | HADDOCK-based drug repurposing screening for COVID-19 | Pre-recorded lecture | Alexandre Bonvin |
| 16:10 – 16:30 | Q&A session | Live | Alexandre Bonvin |
| Day 5 – Friday 26 June 2020 | |||
| 09:00 – 09:40 | Free energy calculations | Pre-recorded lecture 1 | Bert de Groot |
| 09:40 – 10:10 | Free energy calculations | Pre-recorded lecture 2 | Vytautas Gapsys |
| 10:10 – 10:30 | Q&A session | Live | Bert de Groot & Vytautas Gapsys |
| 10:30 – 11:00 |
Coffee and tea break |
||
| 11:00 – 13:00 | Tutorial: PMX | Live | Bert de Groot & Vytautas Gapsys |
| 13:00 – 14:00 | Break | ||
| 14:00 – 14:20 | Alchemy for protein-protein binding | Vytautas Gapsys | |
| 14:20 – 14:40 | Q&A session | Live | Vytautas Gapsys |
| 14:40 – 15:10 |
Final questions, remarks and feedback |
Live | |
Contact
Michelle Mendonca
mmendonca@ebi.ac.uk
