WeNMR / HADDOCK - Information driven modelling of biomolecular complexes

Use Case overview: 

Given the computational demands of the HADDOCK user group, the availability of easily accessible, affordable compute resources is important. The portal is used by a large worldwide community and availability/reliability of the service is crucial. The Helix Nebula science cloud would provide the opportunity to add these resources in a way that is seamless and invisible to the end user. To obtain this outcome, the resources in the Helix Nebula cloud would need to be made available to the current job scheduler of the HADDOCK project.


A version of the HADDOCK portal portable to all cloud providers in Helix Nebula science cloud should be created.

Longterm objectives are:

  • Availability of a service that is independent of a single datacenter or infrastructure.
  • Failover scenarios.
  • Long-term sustainability.
  • Larger amount of available compute resources.
  • Scalability to efficiently handle growth/fluctuations in usage of the service
The challenge

HADDOCK (High Ambiguity Driven protein-protein DOCKing) uses an information-driven, flexible docking approach for the modelling of biomolecular complexes. HADDOCK is distinct from other ab-initio docking methods in that it encodes information from identified or predicted protein interfaces into ambiguous interaction restraints (AIRs) to drive the docking process. HADDOCK can handle a wide class of modelling problems including protein-protein, protein-nucleic acids and protein-ligand complexes.

The HADDOCK portal currently runs on baremetal on two servers at Utrecht University. The front-end of the server is being rewritten in the Flask framework and will be deployed modularly using docker-compose, which should facilitate virtualisation/porting. The machinery behind the front-end requires sufficient computational resources to perform the actual computation. Ideally,  the entire HADDOCK portal could be virtualized on the HNSciCloud infrastructure.

Benefits and impact

The main impact of deploying the heavily-used HADDOCK portal on a hybrid public-commercial cloud will be two-fold:

  1. Ensuring the continuity of the service, especially if grid computing becomes obsolete.
  2. Enabling the provision of a self-contained server which could be used exclusively by interested commercial users (privacy and security are issues here, especially for pharmaceutical companies, which in most cases are not allowed to use external services).

There are currently over 10,000 users worldwide.

Supporting organization: 

SURFsara brings together research and advanced ICT. We do this with a passion for scientific research in our DNA and the extensive expertise provided by our high-performance infrastructure. This enables us to facilitate scientific research while developing initiatives for the business community.

Use Case: 
Life Sciences

Who's behind HNSciCloud?

HNSciCloud Pre-Commercial Procurement is driven by ten leading research organisations from across Europe.