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Integrative structural biology: solving molecular puzzles – Course and Conference Office

EMBO Practical Course

Integrative structural biology: solving molecular puzzles

Overview

Course overview

Integrative structural biology has become a key strategy for determining the structure of biological macromolecules and their complexes. This method entails characterising the 3D structure through an array of complementary techniques, subsequently combining the data to form a consensus model using computational methodologies.

This practical course offers a hands-on introduction to integrative structural biology. Participants will delve into the fundamentals of various experimental structure determination techniques including X-ray crystallography, cryo-EM, small-angle X-ray scattering, NMR, and mass spectrometry, through both lectures and practical exercises. Experts in the field will guide participants on how to analyse and interpret experimental data, and construct structural models across different resolution scales. A significant aspect of the course includes exploring how integrative structural biology addresses limitations of Artificial Intelligence-based structure prediction methods in modelling large complexes and their functional conformations. It will also highlight the emerging field of integrative structural biology of biomolecular complexes visualised directly in their cellular context.

The course location at the European Molecular Biology Laboratory in Hamburg and the Center for Structural Systems Biology on the DESY campus will provide on-site synchrotron SAXS and MX beamlines for training. A guided visit to the European XFEL site is also included in the programme.

Audience

Participants in the early stage of their research careers (Ph.D. students and early postdocs) will be given preference based on their motivation letter. Preference will also be given to applicants who:

i) are entering the field of integrative structural biology

ii) plan to integrate multiple structural techniques within their own projects or plan to develop integrative modeling methods

iii) work on projects that will clearly benefit from an integrative approach.

Modules/resources

  • Introduction to the course
  • Collecting the pieces
  • Putting the pieces together using electron microscopy
  • Putting the pieces together using SAXS
  • Integrative structural dynamics
  • Stitching the pieces together
  • Greater than the sum of parts: integrative modeling

Learning outcomes

This edition will train the participants to explore innovative strategies and techniques in integrative structural biology to overcome these limitations. this course equips a new generation of interdisciplinary structural biologists with the necessary skills to push the boundaries of the field. Through lectures, practical sessions, and collaborative interactions, participants gain insights into the latest advancements and develop a holistic understanding of integrating diverse structural biology techniques.

Speakers

Speakers, trainers, and staff

Tom Burnley

Science and Technology

Facilities Council

UK

Melissa Graewert

EMBL Hamburg

Germany

Maarten Joosten

Delft University of Technology

The Netherlands

Ezgi Karaca

Izmir Biomedicine and

Genome Center (IBG)

Turkey

Karen Manalastas-Cantos

Leibniz Institute of Virology

Germany

Tom Mulvaney

Leibniz Institute of Virology

Germany

Riccardo Pellarin

Microbiologie moléculaire et

biochimie structurale

(MMSB-UMR 5086 CNRS)

France

Scientific organisers

Arjen Jakobi

Kavli Institute of Nanoscience

The Netherlands

Course organisers

Luana Ribeiro

Course and Conference Officer

EMBL Heidelberg

Germany

Irena Provaznikova

Scientific Training Officer

EMBL Heidelberg

Germany

Programme

Are you on social media? Post using #EMBOStructBio and don’t forget to tag @EMBLEvents.

  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – 17 November 2024
Time (Europe/Berlin)Speaker
18:00Arrival to the hotels
Day 2 – 18 November 2024
Time (Europe/Berlin)Speaker
08:15 – 09:15Registration
09:15 – 10:00Welcome & Introductions
Jan Kosinski – EMBL Hamburg, Germany
Arjen Jakobi – Kavli Institute of Nanoscience, The Netherlands
Maya Topf – CSSB/LIV/UKE, Germany
10:00 – 11:00Lecture: Integrative structure determination
Jan Kosinski – EMBL Hamburg, Germany
11:00 – 11:30Coffee Break
11:30 – 12:30Lecture: Integrative in-cell structural biology of cilia and IFT biology
Gaia Pigino – Human Technopole, Italy
12:30 – 14:00Lunch
14:00 – 17:00eXFEL team: Excursion to the European XFEL
17:00 – 19:00Student Talks
19:00 – 22:00Dinner and Discussion
Day 3 – 19 November 2024
Time (Europe/Berlin)Speaker
08:55 – 09:00Overview of the day
Jan Kosinski – EMBL Hamburg, Germany
09:00 – 10:00Lecture: Introduction to X-ray crystallography
Thomas Schneider – EMBL Hamburg, Germany
10:00 – 10:15Coffee Break
10:15 – 11:15Lecture: Protein structure prediction
Mohammed AlQuraishi – Columbia University, USA
11:15 – 11:30Short break and meet the speakers
12:00 – 13:00Lunch
13:00 – 16:00Practical Session

Pratical A: X-ray crystallography demo
Isabel Bento – EMBL Hamburg, Germany
Thomas Schneider – EMBL Hamburg, Germany

Pratical B: Modeling with AlphaFold
Agnieszka Obarska-Kosinska – MPI for Biophysics Frankfurt, Germany
Dmitry Molodenskiy – EMBL Hamburg, Germany
16:00 – 16:15Coffee Break
16:15 – 19:15Practical Session

Practical B: Modeling with AlphaFold
Agnieszka Obarska-Kosinska – MPI for Biophysics Frankfurt, Germany
Dmitry Molodenskiy – EMBL Hamburg, Germany

Practical A: X-ray crystallography demo

Isabel Bento – EMBL Hamburg, Germany
Gleb Bourenkov – EMBL Hamburg
19:15 – 20:30Dinner and Discussion
20:30 – 22:00Student Talks
Day 4 – 20 November 2024
Time (Europe/Berlin)Speaker
08:55 – 09:00Overview of the day
Arjen Jakobi – Kavli Institute of Nanoscience, The Netherlands
09:00 – 10:00Lecture: Introduction to Electron Microscopy
Giulia Zanetti – UCL/Birkbeck/Crick, UK
10:00 – 11:00Lecture: Fitting to EM maps
Maya Topf – CSSB/LIV/UKE, Germany
11:00 – 11:30Coffee Break
11:30 – 12:30Lecture: Model refinement to X-ray and EM data
Arjen Jakobi – Kavli Institute of Nanoscience, The Netherlands
12:30 – 14:00Lunch & Career Session
14:00 – 14:30Lecture: Model validation
Agnel Joseph – Science and Technology Facilities Council, UK
14:30 – 17:00Practical Session C: Rigid and flexible fitting into cryoEM maps
Maya Topf – CSSB/LIV/UKE, Germany
Guendalina Marini – UKE, Germany
Tom Mulvaney – Leibniz Institute of Virology, Germany
Agnel Joseph – Science and Technology Facilities Council, UK
17:00 – 17:15Coffee Break
17:15 – 19:45Practical Session D: High-resolution model refinement
Arjen Jakobi – Kavli Institute of Nanoscience, The Netherlands
Tom Burnley – Science and Technology Facilities Council, UK
Agnel Joseph – Science and Technology Facilities Council, UK
Maarten Joosten – Delft University of Technology, The Netherlands
19:45 – 22:00Dinner and Discussion
Day 5 – 21 November 2024
Time (Europe/Berlin)Speakers
08:55 – 09:00Overview of the day
Maya Topf – CSSB/LIV/UKE, Germany
09:00 – 10:00Lecture: Introduction to SAXS
Melissa Graewert – EMBL Hamburg, Germany
10:00 – 11:00Lecture: Modeling based on SAXS
Cy Jeffries – EMBL Hamburg, Germany
11:00 – 11:30Coffee Break
11:30 – 12:15Practical Session

Practical E: SAXS measurements
Cy Jeffries – EMBL Hamburg, Germany
Aleksi Sutinen – MBL Hamburg, Germany

Practical F: SAXS data analysis
Melissa Graewert – EMBL Hamburg
Dmitry Molodenskiy – EMBL Hamburg, Germany
12:15 – 13:00Practical Session

Practical F: SAXS data analysis
Melissa Graewert – EMBL Hamburg
Dmitry Molodenskiy – EMBL Hamburg, Germany

Practical E: SAXS measurements

Cy Jeffries – EMBL Hamburg, Germany
Aleksi Sutinen – MBL Hamburg, Germany
Aleksi Sutinen – MBL Hamburg, Germany
13:00 – 14:30Lunch
14:30 – 18:00Practical Session G: Integrative modelling using SAXS data
Melissa Graewert – EMBL Hamburg, Germany
Dmitry Molodenskiy – EMBL Hamburg, Germany
18:00 – 22:00Poster Session with drinks and pizza dinner
Day 6 – 22 November 2024

Time (Europe/Berlin)Speaker
08:55 – 09:00Overview of the day
Arjen Jakobi – Kavli Institute of Nanoscience, The Netherlands
09:00 – 10:00Lecture: Molecular dynamics simulations
Syma Khalid – University of Oxford, UK
10:00 – 11:00Lecture: Structure determination of large complexes using NMR and cryo-EM
Rina Rosenzweig – Weizmann Institute, Israel
11:00 – 11:30Coffee Break
11:30 – 12:30CSSB EM facility tour and imaging “show and tell”
by CryoEM facility staff
12:30 – 14:00Lunch
14:00 – 17:00Social event: Tour to HafenCity and a harbor boat trip (optional)
or Free afternoon (optional discussions with tutors)
Day 7 – 23 November 2024
Time (Europe/Berlin)Speaker
08:55 – 09:00Overview of the day
Maya Topf – CSSB/LIV/UKE, Germany
09:00 – 10:00Lecture: Mass spectrometry techniques in structural and cell biology
Fan Liu – FMP Berlin, Germany
10:00 – 11:00Lecture: Crosslink-guided modeling
Riccardo Pellarin – Microbiologie moléculaire et biochimie structurale, France
11:00 – 11:30Coffee Break
11:30 – 12:30Lecture: Integrative modeling with Haddock
Alexandre Bonvin – Utrecht University, The Netherlands
12:30 – 14:00Lunch
14:00 – 16:00Practical Session H: Integrative modeling with HADDOCK – part 1
Ezgi Karaca – Izmir Biomedicine and Genome Center, Turkey
Alexandre Bonvin – Utrecht University, The Netherlands
Dmitry Molodenskiy – EMBL Hamburg, Germany
16:00 – 16:30Coffee Break
16:30 – 19:30Practical Session H: Integrative modeling with HADDOCK – part 2
Ezgi Karaca – Izmir Biomedicine and Genome Center, Turkey
Alexandre Bonvin – Utrecht University, The Netherlands
Dmitry Molodenskiy – EMBL Hamburg, Germany
19:30 – 21:00Dinner and Discussion
Day 8 – 24 November 2024
Time (Europe/Berlin)Speaker
08:55 – 09:00Overview of the day
Jan Kosinski – EMBL Hamburg, Germany
09:00 – 10:30Practical Session I: AI-powered integrative modeling – part 1 using Assembline, RoseTTAFold, AlphaLink, XLMS tools and TEMPy-ReFF
Jan Kosinski – EMBL Hamburg, Germany
Maya Topf – CSSB/LIV/UKE, Germany
Dmitry Molodenskiy – EMBL Hamburg, Germany
Agnieszka Obarska-Kosinska – MPI for Biophysics Frankfurt, Germany
Riccardo Pellarin – Microbiologie moléculaire et biochimie structurale, France
Karen Manalastas-Cantos – Leibniz Institute of Virology, Germany
Thomas Mulvaney – Leibniz Institute of Virology, Germany
10:30 – 11:00Coffee Break
11:00 – 12:00Practical Session I: AI-powered integrative modeling – part 2 using Assembline, RoseTTAFold, AlphaLink, XLMS tools and TEMPy-ReFF
Jan Kosinski – EMBL Hamburg, Germany
Maya Topf – CSSB/LIV/UKE, Germany
Dmitry Molodenskiy – EMBL Hamburg, Germany
Agnieszka Obarska-Kosinska – MPI for Biophysics Frankfurt, Germany
Riccardo Pellarin – Microbiologie moléculaire et biochimie structurale, France
Karen Manalastas-Cantos – Leibniz Institute of Virology, Germany
Thomas Mulvaney – Leibniz Institute of Virology, Germany
12:00 – 13:30Lunch
13:30 – 16:00Practical Session I: AI-powered integrative modeling – part 3 using Assembline, RoseTTAFold, AlphaLink, XLMS tools and TEMPy-ReFF
Jan Kosinski – EMBL Hamburg, Germany
Maya Topf – CSSB/LIV/UKE, Germany
Dmitry Molodenskiy – EMBL Hamburg, Germany
Agnieszka Obarska-Kosinska – MPI for Biophysics Frankfurt, Germany
Riccardo Pellarin – Microbiologie moléculaire et biochimie structurale, France
Karen Manalastas-Cantos – Leibniz Institute of Virology, Germany
Thomas Mulvaney – Leibniz Institute of Virology, Germany
16:00 – 17:00Summary & Round Table including discussion on
responsible conduct of research
17:00 – 19:00Break, free time
19:00 – 22:00Dinner and Discussion

Practical information

Registration fees and motivation letter

The course is limited to 16 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration fees include admission, course materials, meals and coffee breaks. This EMBO course includes accommodation and transportation to and from the DESY Guest House to the venue.

Academia€250
PhD Student€250
Industry€1000

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Financial assistance

Limited financial assistance is provided in the form of registration fee waivers, travel grants and childcare grants

Your place in the meeting is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

– up to €400 for participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter or child-care facility and travel costs for a caregiver. Please note that priority will be given to early-stage researchers. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.

Application

You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of registration fee waivers and travel grants during the motivation letter or abstract selection process. Results will be announced approximately 6 – 8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the meeting. Selection for registration fee waivers and travel grants is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Childcare grants will be allocated in the same timeframe (6-8 weeks before the event start date). Please note that priority will be given to early-stage researchers.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.

Accommodation and transport

Reservations for single room accommodation at the DESY hostel have been made. Note, accommodation is included in the registration fee. The guest house is within a few minutes’ walk from the EMBL laboratories and P12 beamline.

Further information

Address: EMBL Hamburg, Notkestraße 85, Buliding 48e, 22607 Hamburg, Germany

From Hamburg airport take line S1 to Othmarschen (18 stops, 45 min), change to bus number 1 towards Rissen or Schenefelder Holt to Zum Hünengrab (DESY) (5 stops, 10 min).

From Hamburg-Altona train station take bus number 1 to Zum Hünengrab (DESY) (15 stops, 25 min). Ticket costs Public Transport: ca. €3.60 and a taxi will be around €45.

Technical requirements and event software

Technical requirements

Below you will find the software and technical requirements for this course.

  • A laptop with preinstalled software will be provided to each participant.

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Sponsors

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Warning

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 17 - 24 Nov 2024

Location: EMBL Hamburg

Venue: EMBL Hamburg (Building 48e, second floor)


Deadline(s):

Closed


Organisers:

  • Arjen Jakobi
    Kavli Institute of Nanoscience, TU Delft, The Netherlands
    • Jan Kosinski
      EMBL Hamburg, Germany
      • Maya Topf
        Leibniz Institute of Virology, University Medical Center Hamburg-Eppendorf, and Centre for Structural Systems Biology (CSSB), Germany

      Contact: Luana Ribeiro

      Download event poster


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