MDDB statement

For the recognition and support of a collaborative effort to create, establish, and maintain a database that allows the localisation, accessibility, interoperability, and reuse of molecular dynamics simulation data.

This would democratise our field and materialise the impact of molecular dynamics simulations on life sciences research.

We invite you to read our statement and support our initiative.

Programme Director, Infrastrtucture Fund

UK Research and Innovation

Molecular simulation, especially molecular dynamics, is one of the fundamental tools for our understanding of chemical and biological systems. Advances in software performance, development of more powerful computers, and improvement of energy functionals have transformed molecular dynamics into a predictive tool can accelerating the design of drugs, biomaterials, nanoparticles, proteins, and nucleic acids. Even more importantly, molecular dynamics has become essential for understanding how biomolecular machines work.

Over nearly half a century of evolution, the scientific community has moved from simulating small biomolecules in simplified environments to studying complete viruses, cellular organelles, and even small cells. In parallel, simulation time has increased from a few picoseconds (10⁻¹² seconds) to milliseconds (10⁻³ seconds), generating long series of structural data (trajectories). The end result is a flood of data that the community does not know how to manage. Funding agencies and scientific journals require the trajectories to be kept, but these typically end up stored on private disks, preventing their reuse by other groups, integration into bioinformatics analysis systems, or use in training artificial intelligence algorithms. This means that vast amounts of data, generated by the massive use of computers (it is estimated that about 15% of High Performance Computing (HPC) resources are used for molecular dynamics calculations), become unusable for scientific progress, even though they continue to occupy space in data centres.

It is time for Europe to create an infrastructure for systematically storing trajectories and providing an analytical framework that enables universal access and facilitates meta-studies – currently impossible, but crucial for training new machine learning algorithms. The UK plays a key role in this field, not only because of its large molecular dynamics community, but also for its pioneering role in the creation of molecular dynamics databases and the development of innovative strategies for information exchange.

This is why we encourage you to support the creation of a European Infrastructure that allows for the rational storage of molecular dynamics data and its subsequent use in global studies. This infrastructure will not only optimise available computing resources but also open new opportunities to deepen our understanding of biomolecular dynamics.

Additional information

Executive Summary

The summary document of the MDDB project and its international impact.

Policy brief

Initial report on the need for MDDB, outlining its core objectives and alignment with existing European initiatives. It highlights the importance of engaging with national roadmaps and the ESFRI framework, emphasising the strategic relevance of MDDB in the landscape of European research infrastructure. Additionally, it presents key strategies to achieve the project’s objectives and advance the development of MDDB.

The need to implement FAIR principles in biomolecular simulations

Document created by the MDDB consortium presenting the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the need for a collaborative effort to create, establish, and maintain a database that enables the location, accessibility, interoperability, and reuse of molecular dynamics simulation data. Such a development would democratise the field and significantly enhance the impact of MD simulations on life sciences research.