The aim of this practical course is to train young researchers in the computational modelling of protein-protein interactions using a variety of data sources, including X-ray crystallography, NMR, SAXS, cross-linking mass spectrometry and Cryo-EM. The course will introduce and make extensive use of common software and e-science portals to facilitate the adoption of the methods and techniques by the students in their everyday work.
The course will provide lectures describing the basics of the methods applied and hands-on training, either using web-based services such as the web interfaces to the HADDOCK, Phyre and SwarmDock method, or using freely available software which will be pre-installed on to the computers in the training suite. The hands-on sessions will allow the students to try the methods on either pre-packaged or their own research data, with a focus on the immediate translation to their own research problems. The course will also address data quality and validation as well as state-of-the-art tools, and will allow students to achieve thorough experience with analysis, including the potential and limitations of the methods.
Prof. Dr. Alexandre M.J.J. Bonvin, email: firstname.lastname@example.org
Venue and host
The workshop will be held at the EMBL European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
This workshop will run from the 1st - 2nd April 2019, starting at lunch time on the Monday. It will run prior to the 7th CAPRI Assessment Meeting, which will also take place at the Wellcome Genome Campus (3rd to 5th April 2019). For information about the venue and the CAPRI meeting please refer to events website.
Please note registration has closed.
Registration is free for participants from INSTRUCT countries and £250 from other countries. Visit the website to find out if you are from a participating INSTRUCT country.
Accommodation is not included in the registration fee. Registrations close 8 March 2019.
Day 1 - 1st April 2019
11:10 Coach from Cambridge Station
12:00 - 13:00 Registration and Lunch
13:00 - 15:00 Introduction to protein-protein docking: sampling and scoring
Practical: Flexible docking with SwarmDock
Paul A. Bates, and Raphael A.G. Chaleil, Francis Crick Institute, London, UK
15:00 - 15:30 Coffee Break
15:30 - 17:30 Integrative structure determination of macromolecular assemblies
Practical: Determination of macromolecular structure using Cryo-EM data
Maya Topf and Sony Malhotra, Institute of Structural and Molecular Biology, London, UK
Day 2 - 2nd April 2019
08:00 Coach from Cambridge
09:00 - 11:00 Introduction to data-driven docking
Practical: Integrative docking with HADDOCK
Alexandre M.J.J. Bonvin and Panos Koukos, Bijvoet Center for Biomolecular Research, Utrecht, NL
11:00 - 11:15 Coffee Break
11:15 - 13:15 Protein-protein binding affinities
Practical: Modelling interaction strength using machine learning
Iain H. Moal, EMBL European Bioinformatics Institute, Cambridge, UK
13:15 - 14:00 Lunch
14:00 - 16:00 Protein structure prediction
Practical: Modelling protein structures and variants: Phyre, PhyreRisk, Missense3D and EzMol
Michael J.E. Sternberg, Lawrence Kelley and Charles Tochukwu, Imperial College London, London, UK
16:00 - 16:15 Coffee Break
16:15 - 18:15 The validation and verification of protein structure.
Practical: Hands-on assessment of structural quality
Gerard Kleywegt, EMBL European Bioinformatics Institute, Cambridge, UK
There will be a free bus service organised to/from the venue in Hinxton to Cambridge Station. Specific details will be sent closer to the date.