Programme – BioExcel Summer school on Biomolecular Simulations

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 

09:20 – 09:40

BioExcel introduction

Live

Marta Lloret Llinares & Alexandre Bonvin
09:40 – 10:30 Participant introductions Live  
10:30 – 11:00 Virtual coffee & tea break
11:00 – 11:40 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 introduction;
Work on your own with support on forum

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 & Paul Bauer
09:35 – 10:05 Basics of molecular dynamics simulations  Pre-recorded lecture 2 Alessandra Villa & Paul Bauer
10:05 – 10:30  Q&A session Live Alessandra Villa & Paul Bauer
10:30 – 11:00 Virtual coffee & tea break
11:00 – 12:30 Tutorial – A guide to perform MD simulation with GROMACS Live 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
15:05 – 15:30 Virtual break
15:30 – 17:00 Tutorial: Protein-Complex MD Setup with Jupyter Notebooks and BioBB Live Adam Hospital & Genís Bayarri
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

10:30 – 11:00

Virtual 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 
13:00 – 14:00 Break
14:00 – 14:15 GROMACS features and future  Pre-recorded lecture 1 Paul Bauer
14:15 – 14:30

GROMACS features and future

Pre-recorded lecture 2 Paul Bauer 
14:35 – 15:00  Q&A session Live Paul Bauer
15:00 – 15:30

Virtual coffee 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 Virtual 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 Virtual coffee break
15:50 – 16:10 Short talk #2  Pre-recorded lecture  
16:10 – 16:30 Q&A session Live  
Day 5 – Friday 26 June 2020
09:00 – 09:40 Free energy calculations  Pre-recorded lecture 1  
Bert de Groot & Vytautas Gapsys
09:40 – 10:10 Free energy calculations  Pre-recorded lecture 2  
Bert de Groot & Vytautas Gapsys
10:10 – 10:30 Q&A session Live Bert de Groot & Vytautas Gapsys
10:30 – 11:00 Virtual 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 HADDOCK-based drug repurposing screening for COVID-19

Pre-recorded lecture

Alexandre Bonvin
14:20 – 14:40 Q&A session Live Alexandre Bonvin
14:40 – 15:10

Final questions, remarks and feedback

Live  

Contact

Michelle Mendonca
mmendonca@ebi.ac.uk