International Symposium on Grids & Clouds (ISGC) 2018
in conjunction with
Frontiers in Computational Drug Discovery (FCDD)

16-23 March 2018, Academia Sinica, Taipei, Taiwan

Workshop on Integrative modelling of biomolecular complexes using HADDOCK

Date: Monday, 9 March 2020

Time: 09:00 – 17:30

Venue: 3F, Building for Humanities and Social Science, Academia Sinica

ORGANIZER

Professor Alexandre Bonvin, Utrecht University, NL
Dr. Shang-Te Hsu, Academia Sinica, TW

Training

Professor Alexandre Bonvin & Professor Brian Jimenez, Utrecht University, NL

Required

Bring your own laptop, and make to have PyMol and Chimera pre-installed, together with a simple ASCII text editor and software to unpack tar archives (e.g. 7-zip)

Description

The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modelling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process.

We have developed for this purpose a versatile flexible information-driven docking approach HADDOCK. HADDOCK can integrate information derived from biochemical, biophysical or bioinformatics methods to enhance sampling, scoring, or both. The information that can be integrated is quite diverse: among others interface restraints from NMR, mutagenesis experiments, or bioinformatics predictions and, recently, cryo-electron microscopy experiments.

The workshop given by Prof. Alexandre Bonvin from Utrecht University, the Netherlands, will consist of lectures and a hands-on session on computers during which participants will learn to use HADDOCK for the modelling for biomolecular complexes through its user-friendly web portal whose development and operations are supported by the BioExcel Center of Excellence for Computational Biomolecular Research and the EOSC-Hub H2020 projects.

The workshop will consist of lectures by Prof. Bonvin and computer practicals. For the computer practicals the participants should bring their own laptop, make sure to pre-install PyMol and Chimera and have a simple text (ASCII) editor.      

Programme

09:00 - 10:30: Lecture by Alexandre Bonvin
General introduction to integrative modelling and HADDOCK
10:30 - 11:00: Coffee break
11:00 - 12:30: Computer practical – part I
Integrative modelling of a large macromolecular assembly using
cross-linking and cryo-EM data
12:30 - 13:30: Lunch
13:30 – 14:30: Lecture by Alexandre Bonvin
HADDOCK advanced topics
14:30 - 15:30: Computer practical II
Integrative modelling of a large macromolecular assembly using
cross-linking and cryo-EM data (continued)
15:30 - 16:00: Coffee break
16:00 - 17:00: Computer practical III
Integrative modelling of a large macromolecular assembly using
cross-linking and cryo-EM data (continued)
17:00 – 17:30: Question and answer session and wrap up

Online tutorials

For participants not yet familiar with HADDOCK we recommend to try to follow on their own before the workshop the following basis HADDOCK tutorial

HADDOCK basic protein-protein docking tutorial: A tutorial demonstrating the use of the HADDOCK web server to model a protein-protein complex using interface information derived from NMR chemical shift perturbation data. This tutorial does not require any Linux expertise and only makes use of our web server and PyMol for visualisation/analysis
http://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-protein-protein-b...

During the workshop we will follow the following advanced tutorial:
Integrative modelling of the RNA polymerase III apo complex: A combination of our DISVIS, POWERFIT and HADDOCK2.4 portals using cross-links and cryo-EM data to model a large macromolecular assembly.
http://www.bonvinlab.org/education/HADDOCK24/RNA-Pol-III/