Biomolecular NMR: Advanced Tools, protein dynamics

Venue & Address

Swedish NMR Centre, University of Gothenburg,
Medicinaregatan 5C, 41390 Gothenburg

Getting there:
From/To Landvetter Airport. Landvetter Airport bus

To plan your trip and buy bus/tram tickets in Gothenburg use the mobile App "Västtrafik To Go"

Target group

PhD students and researchers with projects involving protein characterization by NMR

Format

Lectures, discussions, and practical hands-on exercises. The lectures will be shared as webinars. The recordings will shared with the registered participants shortly after the session ends.

Webinars
https://gu-se.zoom.us/j/63448914100?pwd=MmI5WTl3MkdRbTF1TGo4eDhScm5CQT09  Passcode: 991893

Organizers and Contacts

Vladislav Orekhov, Göran Karlsson; Chemistry & Molecular Biology & Swedish NMR Centre, University of Gothenburg, Sweden
Contact: e-mail to bionmr.snc@gmail.com

Registration

Please contact bionmr.snc@gmail.com to register for the lecture webinars.

Information

Will be posted e-mailed to the registered participants and found at at https://www.gu.se/en/nmr/workshops-courses-and-conferences

Course Certificates and ECTS credit points

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.

Program

Course teachers

AB -    Andrew Baldwin (University of Oxford, UK)

GB -    Guillaume Bouvignies,  (Ecole Normale Superieure , Paris, France)

TB -    Théodore Bellon (Ecole Normale Superieure , Paris, France)

AJ -    Amir Jahangiri (University of Gothenburg, Sweden)

GK -    Göran Karlsson (Swedish NMR Centre, University of Gothenburg, Sweden)

IK -    Ilya Kuprov, (University of Southampton, UK)

MM -    Maxim Mayzel, (Buker Biospin, Switzerland)

LM -    Luca Mureddu (University of Leicester, UK)

VO -    Vladislav Orekhov (University of Gothenburg, Sweden)

AP -    Alexandra Pozhidaeva (University of Connecticut, Health Center, NMRbox, USA)

GV -    Geerten W. Vuister (University of Leicester, UK)

Topics

CCPN tools for protein NMR: assignment, dynamics, etc

Protein dynamics, theory and practical tools

ChemEx analysis of NMR chemical exchange data

SpinHub project

NMRbox tools

Experimental setup and analysis: Dynamic Centre and Python

AI in NMR spectra processing

Time (CEST)    Title    Type    Teachers

Monday Sep 30  Vladislav Orekhov, Göran Karlsson, Alexandra Pozhidaeva, Amir Jahangiri
  8.40 – 9.00    (on-site only) Registration and Coffee, setting up computers.
  9.00 – 10.50    Welcome, information & student presentations (3-5 min/student)    VO
10.50 – 11.10    Coffee break    
11.00 – 12.10    NMRbox: toolbox for structural biologists,
High Throughput Computing with HTCondor    Lecture    AP
12.20 – 13.00    Lunch        
13.00 – 14.40    NMRbox: AlphaFold and GROMACS tutorial    hands-on     AP
14.40 – 15.00    Coffee break    
15.00 – 18:00    AI in NMR spectra processing hands-on     VO, AJ

18:00– 19.30    (on-site only) Get-together     SNC    

Tuesday Oct 1  Geerten W. Vuister, Luca Mureddu
09.00 – 09.20    Introduction into CcpNmr,       Lecture    GV
09.20 – 10.50    CcpNmr Backbone Assignment Tutorial-part-1,     hands-on    GV,LM
10.10 – 10.30    Coffee break    
10.30 – 11.40    CcpNmr Backbone Assignment Tutorial-part 2,      hands-on     GV,LM
11:40 – 12.40    Introduction into NMR relaxation,       Lecture    GV

12.40 – 13.50    Lunch
        
13.50 – 14.40    CcpNmr Dynamics Tutorial-part-1,       hands-on     GV,LM
14.40 – 15.00    Coffee break    
15.00 – 17:30    CcpNmr Dynamics Tutorial-part-2,     hands-on     GV,LM

Wednesday Oct 2 Ilya Kuprov, Mini-conference

08.40 – 09.30    From biological neuron to a digital one – how neural networks were invented    Lecture    IK

Mini-conference. Insights on  protein motions by NMR (2045 T Bjurström, Medicinareg. 3B)
Chair: Göran Karlsson (Swedish NMR Centre, University of Gothenburg, Sweden)
09.40 – 10.00    Coffee
10.00 – 10.30    Title: TBA
Andrew Baldwin (University of Oxford, UK)
10.30 – 11.00    Illuminating the Unseen: NMR Approaches for Rare Protein States and Challenging Complexes
Guillaume Bouvignies, (Ecole Normale Superieure , Paris, France)
11.00 – 11.30    Protein NMR assignment by isotope pattern recognition
Ilya Kuprov, (University of Southampton, UK)
11.30 – 12.00    Assessing and exploiting conformational dynamics.
Geerten W. Vuister
12.00 – 13.00    Lunch
13.00 – 13.30    Title: TBA
Vladislav Orekhov (University of Gothenburg, Sweden)
13.30 – 14.00    NMRhub: Democratizing NMR
Alexandra Pozhidaeva (University of Connecticut, NMRbox, USA)
14.00– 14.30    Title: TBA
Björn Burmann (University of Gothenburg, Sweden)

Course continues -----------------
Ilya Kuprov    
15.00 – 17.30    How to train and interpret a simple magnetic resonance data processing network    hands-on     IK

Thursday Oct 3   Andrew Baldwin, Maxim Mayzel
09.00 – 09.50    SpinHub project        Lecture,     AB
09.50 – 10.10    Coffee break    
10.10 – 12.40    SpinHub project        hands-on     AB
12.40 – 14.00    Lunch        
14.00 – 14.50    Practical aspects of relaxation experiment setup, acquisition and analysis in Topspin and Dynamics Center, Lecture,             MM
14.50 – 15.10    Coffee break    
15.10 – 17.10    Practical aspects of relaxation experiment setup, acquisition and analysis in Topspin and Dynamics Center, hands-on,             MM

Friday Oct 4  Guillaume Bouvignies
09.00 – 09.50    ChemEx: analysis of NMR chemical exchange data,    Lecture     GB
09.50 – 10.10    Coffee break    
10.10 – 12.30    ChemEx: analysis of NMR chemical exchange data    hands-on     GB, TB
12.40 – 13.30    Lunch        
13.40 – 16:00    Cleaning up hands-on reports        GB, AJ, MM, ??