Biomolecular NMR: Advanced Tools, AI perspective
Research
An advanced hands-on workshop (equiv to 3 ECTS)
Workshop
An advanced hands-on workshop (equiv to 3 ECTS)
Swedish NMR Centre, University of Gothenburg,
Medicinaregatan 5C, 41390 Gothenburg
Getting here:
From/To Landvetter Airport. Landvetter Airport bus https://www.flygbussarna.se/en/landvetter
To plan your trip and buy bus/tram tickets in Gothenburg use mobile App "Västtrafik To Go"
https://gu-se.zoom.us/j/63448914100?pwd=MmI5WTl3MkdRbTF1TGo4eDhScm5CQT09
Passcode: 991893
The lectures will be recorded and shared with the registered participants shortly after the session ends.
PhD students and researchers with projects involving protein characterization by NMR
Lectures, discussions, and practical hands-on exercises.
Vladislav Orekhov, Göran Karlsson; Chemistry & Molecular Biology & Swedish NMR Centre, University of Gothenburg, Sweden
Contact: e-mail: bionmr.snc@gmail.com
Registration is closed. Subsidized accommodation in double rooms is available. Please indicate if you need it.
(only for the students registered for the tutorial hands on sessions)
Since this course will use NMRbox for the tutorial sessions, you must obtain an account (if you do not have it) at NMRbox.org . Then, please register for the course at at https://nmrbox.nmrhub.org/events
You find an intro about NMRbox by Dr. Adam Schuyler at
https://api.nmrhub.org/files/120/326/nmrbox22-2-NMRbox-intro-schuyler.mp4
https://www.gu.se/en/nmr/workshops-courses-and-conferences
In order to fully accomplish the course, the student should attend all tutorial lectures and practical sessions. For every tutorial session a short report should be submitted as outlined by the session instructors. After acceptance of the lab reports by the instructors, the course certificate can be requested by e-mail to bionmr.snc@gmail.com.
SB - Simon Bruderer (Buker Biospin, Switzerland)
MB - Marek Bukowicki (University of Warsaw, Poland)
BMB - Björn Marcus Burmann (University of Gothenburg)
CM - Charles Burridge (University of Gothenburg)
PG - Peter Güntert (ETH, Switzerland)
PK - Piotr Klukowski (ETH, Switzerland)
AJ - Amir Jahangiri (University of Gothenburg, Sweden)
SJ - Sylwia Jopa (University of Warsaw, Poland)
KK - Krzysztof Kazimierczuk (University of Warsaw, Poland)
JHL - Jung Ho Lee (Seoul National University, Korea)
VO - Vladislav Orekhov (University of Gothenburg)
ZZ - Zhidian Zhang (MIT, USA)
| date | 9:00 AM – 12:00 AM | 1:00 PM – 6:00 PM |
| Mon 29th | Intro, student presentations | ZZ |
| Tue 30th | PG, PK | VO, AJ |
| Wed 1st | JHL | SB |
| Thu 2nd | Mini-conference | KK |
| Fri 3rd | BMB | Reports and clean ups |
Topics
• Automated Assignment and Structure
• AI in NMR spectra processing
• Machine learning for structure prediction and design
• Integrating experimental results for structure prediction
• Protein dynamics by NMR
• ShimNet: a neural network for post-acquisition shimming
| Time (CEST) | Title | Type | Teachers |
|---|---|---|---|
| Monday Sept 29th | |||
| 08:40–09:00 | (on-site only) Registration and Coffee, setting up computers. | ||
| 09:00–10:50 | Welcome, information & student presentations (5-10 min/student) | VO, GK | |
| 10:50–11:10 | Coffee break | ||
| 11:10–12:10 | Student presentations | ||
| 12:30–13:00 | Lunch | ||
| 13:10–14:50 | Machine learning for structure prediction and design | Lecture | ZZ |
| 14:50–15:10 | Coffee break | ||
| 15:10–18:00 | Machine learning for structure prediction and design | Hands-on practical | ZZ |
| 18:00–19:30 | (on-site only) Get-together | ||
| Tuesday Sept 30th | |||
| 09:00–09:40 | Automated biomolecular NMR spectra analysis with ARTINA and NMRtist | Lecture | PG |
| 09:40–12:20 | ARTINA and NMRtist | Hands-on practical | PG, PK |
| 10:10–10:30 | Coffee break | ||
| 12:30–13:30 | Lunch | ||
| 13:30–14:30 | Next generation spectra processing with AI | Lecture | VO, AJ |
| 14:30-14:50 | Coffee break | ||
| 14:50–17:00 | Next generation spectra processing with AI | Hands-on practical | VO, AJ |
| Wednesday Oct 1st | |||
| 09:00-09:50 | Rotational Diffusion of a Dimeric Protein | Lecture | JHL |
| 09:50–10:10 | Coffee break | ||
| 10:10–12:20 | Modelfree and Rotdif | Hands-on practical | JHL |
| 12:30–14:00 | Lunch | ||
| 14:00–14:50 | Deep learning in TopSpin for processing of 1d and 2d spectra | Lecture | SB |
| 14:50–15:10 | Coffee break | ||
| 15:10–17:10 | Deep learning in TopSpin for processing of 1d and 2d spectra | Hands-on practical | SB |
| Thursday Oct 2nd | Mini-conference: Deep Learning Reshapes NMR Spectroscopy Venue: Sydamerika, Wallenberg Conference Center, Medicinareg 20 A | ||
| Chair: Göran Karlsson (Swedish NMR Centre, University of Gothenburg, Sweden) | |||
| 08:30–09:00 | Coffee | ||
| 09:00–09:30 | Charting the Future: How Deep Learning Is Transforming NMR Spectroscopy Piotr Klukowski (ETH, Switzerland) | ||
| 09:30–10:00 | Neural network for processing variable-temperature non-stationary 2D NMR data Marek Bukowicki (University of Warsaw, Poland) | ||
| 10:00–10:30 | What Have Protein Language Models Learned? Zhidian Zhang (MIT, USA) | ||
| 10:30–11:00 | Real-Time NMR Monitoring of Protein Aggregation by Inertia-Driven Agitation Jung Ho Lee (Seoul National University, Korea) | ||
| 11:00–11:30 | Deep learning in TopSpin for processing of 1d and 2d spectra Simon Bruderer (Bruker Biospin, Switzerland) | ||
| 11:30–12:00 | AI in NMR and Structural Biology Vladislav Orekhov (University of Gothenburg, Sweden) | ||
| 12:00–12:30 | Bacterial OMVs as novel tools for the in-situ characterisation of bacterial envelope proteins Björn Marcus Burmann (University of Gothenburg) | ||
| 12:30–13:30 | Lunch (Wallenberg Conference Centre) | ||
| 13:30–14:40 | Poster session (Wallenberg Conference Centre) | ||
| Course continues at the Swedish NMR centre | |||
| 15:00–15:40 | Correcting lineshape distortions using ShimNet | Lecture | KK |
| 15:40–17:30 | Correcting lineshape distortions using ShimNet | Hands-on practical | KK, SJ |
| Friday Oct 3rd | |||
| 09:00–09:50 | Different flavours of protein dynamics to study large protein complexes | Lecture | BMB |
| 09:50–10:10 | Coffee break | ||
| 10:10–12:30 | 19F-NMR: Spectral deconvolution, measurements of dynamics and analysis. | Hands-on practical | BMB |
| 12:30–13:30 | Lunch | ||
| 13:40–16:00 | Cleaning up, hands-on reports |