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Virtual Research Environment for Integrative Modelling of Biomolecular Complexes

HADDOCK Worldwide user map,

Computational structural biology has provided valuable insights to many research fields into the complex and intricate network of interactions between macromolecules. Our software HADDOCK ( is contributing to shedding light on those interactions, being used by 26500 + users worldwide, including pharma companies, via command-line or webserver. There are two main limitations that hamper further development and efficient use of HADDOCK: 1) Its core protocol is a static workflow, which hinders its expansion and incorporation into custom pipelines; 2) Its operation mode is geared towards HTC (grid/local) resources, which prevents scaling to thousands of runs and efficient use of Cloud resources.

We aim to address these limitations by developing a customizable, interactive, HTC/Cloud(and HPC)-optimized and reusable Virtual Research Environment for Integrative Modelling of Biomolecular Complexes which will consist of three main layers: A workflow builder/manager, an execution middleware, and an analysis, storage and sharing infrastructure. It will stimulate the integration of third-party software. When possible, existing solutions from the eScience Research Software directory will be reused.

By integrating all steps involved in studying biomolecular interactions,thisVREwill lower the steep learning curve for researchers and students from different fields and contribute to reproducible research and FAIR sharing of data.

Participating organisations

Life Sciences
Netherlands eScience Center
Utrecht University


Peter Kalverla
Peter Kalverla
Fakhereh (Sarah) Alidoost
Fakhereh (Sarah) Alidoost
Alexandre M.J.J. Bonvin
Principal investigator
Utrecht University
João M. Correia Teixeira
Utrecht University
Pablo Lopez-Tarifa
eScience Coordinator
Netherlands eScience Center
Rodrigo Vargas Honorato
Principal investigator
Utrecht University
Stefan Verhoeven
Stefan Verhoeven
eScience Research Engineer
Netherlands eScience Center

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