Instruct-ERIC Events

Joint INSTRUCT-CAPRI Workshop on Integrative Modelling of Protein-Protein Interactions

Date: 01-Apr-2019 to 02-Apr-2019

Contact: Alexandre Bonvin



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:

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

18:00 Dinner

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

Coach Service

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.

EMBL-EBI Hinxton, United Kingdom

Joint INSTRUCT-CAPRI Workshop on Integrative Modelling of Protein-Protein Interactions