Alexandre Bonvin bio photo

Computational Structural Biology group focusing on dissecting, understanding and predicting biomolecular interactions at the molecular level.

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INSTRUCT practical course

Advanced methods for the integration of diverse structural data with NMR data – 2nd Edition

Aims of the course

The course aims at training young researchers in the combined use of NMR data with other structural biology techniques, such as SAXS, X-ray diffraction or Cryo-EM in order to understand and rationalize the structural and dynamical properties of macromolecular systems. In addition, this course will introduce and make extensive use of user-friendly e-science portals to facilitate the adoption of the methods and techniques by the students in their everyday work.

This INSTRUCT course will provide lectures describing the basics of the methods applied and hands-on training with the intuitive, web-based services of the WeNMR infrastructure, in collaboration with the MoBrain Competence Center, the West-Life VRE and the BioExcel center of excellence H2020 EU projects, with the support of SURFSara, which is part of the MoBrain CC and is supporting us in the organisation of this course. The hands-on sessions will allow the students to try the methods on either pre-packaged or their own research data. The course will address state-of-the-art tools and facilities. Participants will be selected among all applicants taking into account the following criteria: previous experience in the field of biomolecular NMR and structure biology; experience in computational aspects of structural biology; gender balance; relevance of current research to the course contents.

Location and dates

  • Event Date: 11th Apr 2016 to 15th Apr 2016
  • Location: SURF Offices Hoog Overborch (Hoog Catharijne), Moreelsepark 48, 3511 EP Utrecht, The NetherlandsPadualaan 8
  • Directions
  • Plan you travel within NL

The course will start on Monday afternoon April 11th and run until lunch time on Friday April 15th, allowing for arrival and departure in the morning/afternoon of the first and last days.

Utrecht can easily be reached from various airports: Several low-cost companies fly into Amsterdam Schiphol, Rotterdam or Eindhoven airports, which are all connected by direct and fast trains to Utrecht (between half an hour to one hour travel time). The SURF location is very close to Utrecht central station.

Application procedure:

Applicants should send to the lead contact (see below) by email a short CV and letter of motivation explaining how they will benefit from attending this course. The deadline for applying is set to February 15th, 2016. Accepted applicants will be notified by March 1st, 2016.

Lead contact

  • Prof. Dr. Alexandre M.J.J. Bonvin – a.m.j.j.bonvin@uu.nl

Number of participants: 20

Course programme

The course will start in the afternoon of April 11th at 13:00 and end at 12:00 on April 15th. Lunch will be provided for all days except the Monday. A detailed programme will be provided at a later stage.

  • April 11 (room 3.1): MS and solution NMR
    • Morning: arrival
    • 13:00-13:10 Welcome + intro (Bonvin)
    • 13:10-13:30 Short intro to HPC/HTC infrastructure and services (SURFSara)
    • 13:30-15:00 Heck: Characterization of large assemblies by mass spectrometry
    • 15:00-15:30 coffee break
    • 15:30-17:00 Boelens: Characterization of macromolecular assemblies by solution NMR

  • April 12 (room 3.3): NMR-based protein structure refinement + integration with SAXS
    • 9:00-10:45: Parigi: Paramagnetic NMR data and integration of SAXS and NMR data for the analysis of protein structure/dynamics
    • 10:45-11:15: coffee break
    • 11:15:13:00: Rosato: Molecular dynamics for NMR-based protein structure refinement
    • 13:00:13:45: Lunch
    • 13:45-17:00: AMPS-NMR + FANTEN + MAXOCC computer practicals (Rosato / Parigi)

  • April 13 (room 3.3): Cryo-EM / Xray
    • 9:00-10:45: Gros: Characterization of macromolecular complexes by X-Ray crystallography and cryo-EM
    • 10:45-11:15: coffee break
    • 11:15-13:00: Carazo: Cryo-EM analysis of biomolecular assemblies
    • 13:00:13:45: Lunch
    • 13:45:17:00: Cyro-EM computer practical (Jose Miguel de la Rosa)
    • Evening: workshop dinner

  • April 14 (room 4.1): Integrative modelling
    • 9:00-10:45: Bonvin: Integrative modelling of biomolecular complexes by docking
    • 10:45-11:15: coffee break
    • 11:15-13:00: Bonvin: Integrative modelling of biomolecular complexes by docking
    • 13:00:13:45: Lunch
    • 13:45:17:00: HADDOCK computer practical (Bonvin + local assistant)

  • April 15 (room 3.3): Solid state NMR lecture + open discussion / question and answers
    • 9:00-10:45: Baldus: Characterization of macromolecular assemblies by solid-state NMR
    • 10:45-11:15: coffee break
    • 11:15-12:15: Open discussion / question and answers
    • 12:15:13:00: Lunch
    • Departure

Note that participants are required to bring their own laptop for the practicals, ideally with applications allowing remote ssh access and also VirtualBox installed to allow for running Virtual Machines that will be provided to the participants so that the students can take them back with them for further analysis/use back home. We will also make use of SURFSara cloud resources for the practicals.

Case studies will be provided via the web for re-examination also at the home lab.

Lecturers:

Costs:

100 euros for participants from Instruct countries (check here), 300 euros for others. The registration fee covers lunches and coffee breaks and the course dinner. Travel and lodging are not included.

Housing information:

A list of hotels, hostels and bed and breakfast possibilities in Utrecht can be downloaded here. Participants are responsible for arranging their own housing.