More than a hundred experts in molecular simulation have published a paper in the journal Nature Methods calling for a paradigm shift in molecular dynamics data management. The paper, led by Modesto Orozco, professor at the University of Barcelona, and the expert Adam Hospital, both members of the Institute for Research in Biomedicine (IRB Barcelona), proposes the creation of a common infrastructure for storing and reusing data in the context of the revolution that artificial intelligence represents.
In particular, the article advocates the implementation of FAIR (findable, accessible, interoperable, reusable) principles to improve the reproducibility of the calculations and facilitate their subsequent use as a source of information on the flexibility of biomacromolecules.
Computational simulations have become a key tool for studying the behaviour of biomolecules over time. Thanks to supercomputers, molecular dynamics (MD) makes it possible to observe these processes with great precision and provide new knowledge of interest both in basic research and in the design of biomolecules, from enzymes to drugs.
Unlike structural biology or genomics - disciplines in which storing and sharing data under common standards is common practice - in the field of molecular simulation these data remain fragmented. Moreover, they often end up forgotten on personal computers, which hinders the reproducibility of calculations and prevents their further use. This creates a major problem in integrating data into structural biology and biophysics workflows, and slows down the development of artificial intelligence methods, the training of which is extremely dependent on access to large amounts of dynamic data.
Reuse rather than repeat
Designing an open and sustainable ecosystem that multiplies the impact of this data and avoids unnecessary duplication is the aim of the new article, signed by more than a hundred leading international researchers, including several Nobel laureates in chemistry. The authors call for a change of model to apply the FAIR principles - which ensure that data is findable, accessible, interoperable and reusable - to simulation results.
"The community has assumed for years that repeating a simulation was easier and cheaper than archiving it. But that is no longer true", says Modesto Orozco, professor at the UB's Faculty of Chemistry, coordinator of the European MDDB project, head of the Molecular Modelling and Bioinformatics Group at IRB Barcelona and founder of the biotechnology company Nostrum Biodiscovery.
"The knowledge we can get from reusing data is enormous: it allows us to identify new targets, train artificial intelligence algorithms or design new experiments", adds researcher Adam Hospital. Orozco and Hospital lead the European MDDB project, funded by the European Commission's Horizon Europe programme, which aims to establish a centralized and accessible database for simulations.
