Biomolecular NMR: Advanced Tools, AI perspective
Forskning
En avancerad praktisk workshop på doktorandnivå (motsv 3 ECTS)
Workshop
En avancerad praktisk workshop på doktorandnivå (motsv 3 ECTS)
Svenskt NMR-centrum, Göteborgs universitet,
Medicinaregatan 5C, 41390 Göteborg
Hitta hit:
Från/till Landvetter Flygplats, Flygbussarna: https://www.flygbussarna.se/en/landvetter
Hita resa och köpa biljett för resa medelst buss eller spårvagn, använd appen "Västtrafik To Go"
https://gu-se.zoom.us/j/63448914100?pwd=MmI5WTl3MkdRbTF1TGo4eDhScm5CQT09
Passcode: 991893
Föreläsningarna kommer spelas in och delges deltagarna kort efter respektive session.
Doktorander och forskare med projekt som involverar proteinkarakterisering med NMR.
Föreläsningar, diskussioner och praktiska övningar..
Vladislav Orekhov, Göran Karlsson; Inst. för kemi och molekylärbiologi & Svenskt NMR-centrum, Göteborgs universitet
Kontakt: e-mail till bionmr.snc@gmail.com
Registreringen är stängd. Subventionerat boende i dubbelrumm finns, indikera om det är något som önskas i ansökningsbrevet.
(bara för deltagare registrerade för praktiska sessioner)
Eftersom kursen kommer att använda NMRbox för de praktiska övningarna krävs ett konto (om man inte redan har ett) på NMRbox.org. Med konto på plats måste man sedan registrera sig för kursen på https://nmrbox.nmrhub.org/events.
Du hittar en introduktion om NMRbox av Dr. Adam Schuyler på
https://api.nmrhub.org/files/120/326/nmrbox22-2-NMRbox-intro-schuyler.mp4.
https://www.gu.se/nmr/workshops-kurser-och-konferenser
För att fullt godkännas på kursen behöver studenten delta på alla tutorialföreläsningar och praktiska övningar. En kort rapport behöver lämnas in efter varje tutorialföreläsning enligt repsektive instruktörs krav. Ett kursintyg kan efterfrågas efter att alla rapporter är godkända genom att e-maila bionmr.snc@gmail.com.
SB - Simon Bruderer (Bruker 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 |