BioExcel Summer School 2023
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Index
Introduction
Welcome to the ‘Living Document’ for this course, which you can use to:
- Take notes collectively
- Ask questions (during lectures, instead ask directly from the lecturer!)
- Share contact information to network with other participants
At the top left you can select the source code, mixed, or html view. If you’re not editing, please switch to html (the eye-icon). The syntax is Markdown (it’s cool) you can also click on the ?-icon at the top banner on the left.
Visit the course handbook for information about relevant links, the course setup and the course programme.
Please, feel free to use this document to make notes, record any questions that you ask and the answers that trainers provide you with. Trainers will answer questions asked in this document, but we cannot guarantee that they do it immediately.
It is a great way of capturing the knowledge exchanged during the course and saving it for future use. Remember - you don’t have to contribute, but any additions will be welcomed!
tags: GROMACS HADDOCK BioBB PMX pizza
📅 Agenda
Click on > Details below to expand that day’s agenda!
Sunday 10th September
| 16:00 - 17:45 | Pick up at airport, badges |
|---|---|
| 18:00 - 19:00 | Bus from airport to Hotel |
| 19:00 - 20:00 | Registration @ Hotel |
| 20:00 | Dinner @ Hotel |
Monday 11th September
| 08:30 - 08:45 | Bus from the hotel to the venue |
|---|---|
| 8:45 - 09:00 | Welcome and introduction (10’) |
| 09:00 - 10:30 | Lecture 1 - MD basics (90’) Alessandra |
| 10:30 - 11:00 | Coffee Break (30’) |
| 11:00 - 12:45 | Tutorial 1: GROMACS (1h45’) |
| 12:45 - 13:00 | lunch (75’) |
| 14:00 - 15:30 | Lecture 2 - Interoperable and reproducible biomolecular simulation workflows using BioBB (90’) Adam |
| 15:30 - 16:00 | Coffee break (30’) |
| 16:00 - 17:45 | Tutorial 2: BioBB (1h45’) [Extra Slides] |
| 17:45-18:00 | Travel back to hotel |
| 18:00-20:00 | Free |
| 20:00 | Dinner @ Hotel |
Tuesday 12th September
| 08:30 - 08:45 | Bus from the hotel to the venue |
|---|---|
| 8:45 - 09:00 | |
| 09:00 - 10:30 | Lecture 3 - Integrative modelling with HADDOCK (90’) Rodrigo |
| 10:30 - 11:00 | Coffee break (30’) |
| 11:00 - 12:45 | Tutorial 3: HADDOCK (1h45’) |
| 12:45 - 13:30 | lunch (45’) |
| 13:30 - 14:30 | Flashtalks (60’) |
| 14:30 - 17:00 | Poster session: ODD numbers presented first, coffee, EVEN numbers (2.5h) |
| 17:00 - 17:15 | Travel back to hotel |
| 17:15 - 20:00 | Free  |
| 20:00 | Dinner @ Hotel |
Wednesday 13th September
| 08:30 - 08:45 | Bus from the hotel to the venue |
|---|---|
| 8:45 - 09:00 | |
| 09:00 - 10:30 | Lecture 4 - Enhanced sampling (90’) Erik |
| 10:30 - 11:00 | Coffee break (30’) |
| 11:00 - 12:45 | Tutorial 4: GROMACS (enhanced sampling, 1h45’ |
| 12:45 - 13:30 | lunch (45’) |
| 13:30 - 15:00 | Lecture 5 - Modeling molecular recognition through enhanced-sampling methods (90’) Attilio |
| 15:00 - 15:30 | Coffee break + group photo (30’) |
| 15:30 - 17:00 | Tutorial 5: EDES (1h45’) |
| 17:00 - 17:15 | Travel back to hotel |
| 17:15 - 20:00 | Free  |
| 20:00 | Dinner @ Hotel |
Thursday 14th September
| 08:30 - 08:45 | Bus from the hotel to the venue |
|---|---|
| 8:45 - 09:00 | |
| 09:00 - 10:30 | Lecture 6 - Free energy calculation Intro and Applications (90’) Bert |
| 10:30 - 11:00 | Coffee break (30’) |
| 11:00 - 12:45 | Tutorial 6: PMX (1h45’) |
| 12:45 - 13:45 | lunch (60’) |
| 13:45 - 14:45 | Lecture 7: QM/MM Emiliano (1h) |
| 14:45 - 16:00 | Poster Discussion (1h + 15min coffee break) |
| 16:00 - 19:00 | Travel and excursion to Nora (3h)  |
| 19:00 - 20:00 | Travel and visit to Pula (1h) |
| 20:00 | Social dinner (Pula) |
Friday 15th September
| 08:30 - 08:45 | Bus from the hotel to the venue |
|---|---|
| 09:00 - 10:00 | Remote AI lecture (AI) Jon Paul online Video recording (60’) |
| 10:00 - 10:30 | Poster prize winner announcement + Coffee break (30’) |
| 10:30 - 11:30 | Career session (60’) |
| 11:30 - 12:30 | feedback survey + final remarks + (60’) |
| 12:30 - 13:30 | lunch (take away for those leaving earlier) (60’) |
| 13:30 - 14:30 | Bus to the airport |
Extra resources
HADDOCK
These are some other tutorials that should fit your research questions!
Basic protein-protein docking, use this one to learn how to setup your docking in the server!
How to screen binding sites in HADDOCK
How to setup your shape-based docking, this will guide you trough the process I showed in the lecture 🤓
If you have any questions or need any extra help, please reach out to us! r.vargashonorato@uu.nl / m.giulini@uu.nl / ask.bioexcel.eu 👨🏽💻
Links
- Web services: wenmr.science.uu.nl
- Group Website: bonvinlab.org
- List of all tutorials: https://www.bonvinlab.org/education/
- GitHub repository of the BonvinLab: github.com/haddocking
- Github repository of HADDOCK3 - contributions are welcome! github.com/haddocking/haddock3