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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.
This article was published in the following journal.
Name: Bioinformatics (Oxford, England)
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A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories applicable to MOLECULAR BIOLOGY and areas of computer-based techniques for solving biological problems including manipulation of models and datasets.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Models connecting initiating events at the cellular and molecular level to population-wide impacts. Computational models may be at levels relating toxicology to adverse effects.
Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.
Statistical models in which the value of a parameter for a given value of a factor is assumed to be equal to a + bx, where a and b are constants. The models predict a linear regression.
Biological therapy involves the use of living organisms, substances derived from living organisms, or laboratory-produced versions of such substances to treat disease. Some biological therapies for cancer use vaccines or bacteria to stimulate the body&rs...
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...
Palliative care is the active holistic care of patients with advanced progressive illness. Management of pain and other symptoms and provision of psychological, social and spiritual support is paramount. The goal of palliative care is achievement of the ...