About the need to make computational models of biological macromolecules available and discoverable.

07:00 EST 13th February 2020 | BioPortfolio

Summary of "About the need to make computational models of biological macromolecules available and discoverable."

We contribute this opinion letter to raise awareness on the fact that very few of the peer-reviewed articles reporting structural models make these models available, and that most modern databases/datasets of models do not allow sequence searches. Free model availability is, like any other methodological material, critical for reproducibility, reuse, reanalysis and criticism, while methods for sequence-based model search are necessary to facilitate model discovery, accessibility and reuse. We argue that model availability should be no exception to science-opening and FAIR policies, and suggest that (i) model deposition should be encouraged, if not made mandatory, by journals and funding bodies, and (ii) the community would benefit from a centralized hub where protein models are discoverable through sequence searches. The main challenge is probably to have all actors (i.e. databases, publishers, funding bodies, possibly even structure prediction competitions and the wwPDB) working together, as the technological and monetary impediments on such endeavor are minor. We have in fact setup, with modest resources and effort, a palliative solution that enables sequence searches for over 5000 protein sequence entries from integrative models, models based on contact predictions, CASP models, and more, linked to the corresponding structural models. Properly managed, a global hub for protein models will allow for deeper capitalization on the recent improvements in protein structure prediction, the rise in tools for and applications of integrative modeling, and the power of modern molecular simulations.


Journal Details

This article was published in the following journal.

Name: Bioinformatics (Oxford, England)
ISSN: 1367-4811


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