WeNMR/HADDOCK workshop at ISGC2021 in Taipei

Monday 22 Mar 2021, 09:00 → 17:30 Europe/Amsterdam

Alexandre Bonvin (eNMR/WeNMR (via Dutch NGI)), Brian Jimenez Garcia (Utrecht University)

Structural biology aims at characterizing the structural (atomic coordinates) and dynamic (fluctuation of atomic coordinates over time) properties of biological macro-molecules. Gaining insight into 3D structures of bio-molecules is critical for understanding the vast majority of cellular processes, with direct application in health and food sciences.

Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the HTC infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects are a now operating as Thematic Services in the EOSC-Hub project (www.eosc-portal.eu), with the HADDOCK portal (haddock.science.uu.nl) sending >10 millions of jobs and using ~4000 CPU-years per year.

Learning goal: 
We will summarize 11 years of successful use of e-infrastructure solutions to serve a large worldwide community of users (>18’000 to date), providing them with user-friendly, web-based solutions that allow to run complex workflows in structural biology. We will in particular share our experience operating and deploying those services from the provider point of view with a focus on sustainability and easy of deployment of the services, making use of containerization technologies.

Agenda:
09:00 - 10:30: General introduction to integrative modelling and HADDOCK
10:30 - 11:00: Coffee break
11:00 - 12:30: Computer practical – part I Modelling antibody-antigen complexes with HADDOCK
12:30 - 13:30: Lunch
13:30 - 14:15: HADDOCK advanced topics 14:15 - 14:30: Short break
14:30 - 15:00: LightDock: An artificial intelligence-based integrative docking platform
15:00 - 16:00: Computer practical – part II Integrative modelling of membrane complexes with LightDock and HADDOCK
16:00 - 16:15: Coffee break
16:00 - 17:00: Computer practical II continued Integrative modelling of membrane complexes with LightDock and HADDOCK (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-proteinprotein-basic

During the workshop we will follow the following tutorials:

• HADDOCK2.4 antibody-antigen docking tutorial: This tutorial demonstrates the use of HADDOCK2.4 for predicting the structure of an antibody-antigen complex using information about the hypervariable loops of the antibody and either the entire surface of the antigen or a loose definition of the epitope. This tutorial does not require any Linux expertise and only makes use of our web servers and PyMol for visualisation/analysis. https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-antibody-antigen/
   
• LightDock+HADDOCK membrane proteins tutorial: This tutorial demonstrates the use of LightDock for predicting the structure of membrane receptor – soluble protein complex using the topological information provided by the membrane to guide the modelling process. The resulting LightDock models are then refined using HADDOCK. https://www.bonvinlab.org/education/HADDOCK24/LightDock-membrane-proteins

 

 

HADDOCK2.4 basic protein-protein docking tutorial