Integrative modelling and simulations in the cloud
Key Organizer: Prof. Alexandre Bonvin, Utrecht University, the Netherlands, a.m.j.j.bonvin@uu.nl
Predicting and characterizing the structure of biomolecular complexes 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 information-driven docking approach HADDOCK (https://www.bonvinlab.org/software), which can integrate information derived from biochemical, biophysical or bioinformatics methods to guide the modelling.
Running such simulations does require access to computational resources. To facilitate its use HADDOCK is offered as a web portal making of the EGI/EOSC resources. In the context of the EuroHPC EU/India collaborative project GANANA (ganana.eu), the new modular version of HADDOCK3 has been installed on the Indian HPC cloud resource (ICECloud: https://icecloud.in).
This workshop will consist of lectures and hands-on computer tutorials consisting of the recent HADDOCK developments and ICECloud features. Demonstration on the use of HADDOCK3 to model an antibody-antigen complexes, through web-based access / Jupyter notebook through ICE-CLOUD. Overview and short demonstrations on GROMACS and molecular docking available through ICE-CLOUD will be given. Participants are encouraged to bring their own problems to get advice on the best modelling strategy.
Summary of workshop format :
The workshop will consist of lectures by Prof. Alexandre Bonvin (Utrecht University), Mr. Ramakrishnan EP (C-DAC Pune) and Ms. Shruti Koulgi and guided computer tutorials during which participants will get experience in using the new modular HADDOCK3 version and get an exposure to ICECloud for structural modeling and analysis. During the tutorials the participants would be able get hands-on on HADDOCK3, GROMACS and molecular docking through the ICECloud resources. Participants are required to bring their own laptops. Knowledge of Linux and command line is required.
