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Enhancing Protein-Drug Binding Prediction

Combining molecular simulation and eScience technologies

Image: Drug binding to receptor protein by Sam Hertig – http://www.samhertig.ch/blog/wp-content/uploads/2015/10/m4v1m2.jpg

Drugs typically exert their effects by binding to proteins. Methods are therefore needed to predict protein-drug binding but efficiently doing so is difficult and requires computationally demanding techniques to appropriately account for the dynamics of the binding process, especially for many pharmaceutically relevant families of enzymes or other proteins.

Overcoming current challenges

This project aims for efficient prediction of protein-drug binding interactions by introducing and combining modelling and eScience technologies. For that purpose molecular simulation methods, algorithms, and efficient computing and data handling techniques will be combined to overcome current methodological challenges. A platform will be introduced that enables combination of such methodologies into eScience workflows for evaluating protein-drug binding in applied settings.

Software platform for discovery and optimization

In this project methodologies will be realized as a heterogeneous and HPC driven eScience platform. For future modelling efforts, handling of large sets of calibration data is crucial. These are available via direct collaborations with academic and industry partners, who have shown strong interest in our eScience and open-source approach. The platform will enable efficient molecular simulation workflows in applied and industrial setting, e.g. in the context of drug discovery and optimization for cancer or other therapy.

Participating organisations

Vrije Universiteit Amsterdam
Netherlands eScience Center
CWI
Life Sciences
Life Sciences

Impact

Output

Team

DG
Daan Geerke
Principal investigator
VU University Amsterdam
Lourens Veen
Lourens Veen
eScience Research Engineer
Netherlands eScience Center
MvD
Marc van Dijk
Postdoctoral researcher
Vrije Universiteit Amsterdam
ME
Martin Engler
Postdoctoral reseacher
Centrum Wiskunde en Informatica
Lars Ridder
Lars Ridder
eScience Coordinator
Netherlands eScience Center
Felipe Zapata
Felipe Zapata
eScience Research Engineer
Netherlands eScience Center

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