{"id":103748,"date":"2025-04-30T12:27:10","date_gmt":"2025-04-30T10:27:10","guid":{"rendered":"https:\/\/www.pcb.ub.edu\/irb-barcelona-is-coordinating-a-study-involving-more-than-a-hundred-experts-to-create-a-fair-database-of-molecular-simulations\/"},"modified":"2025-04-30T17:10:35","modified_gmt":"2025-04-30T15:10:35","slug":"irb-barcelona-is-coordinating-a-study-involving-more-than-a-hundred-experts-to-create-a-fair-database-of-molecular-simulations","status":"publish","type":"post","link":"https:\/\/www.pcb.ub.edu\/en\/irb-barcelona-is-coordinating-a-study-involving-more-than-a-hundred-experts-to-create-a-fair-database-of-molecular-simulations\/","title":{"rendered":"IRB Barcelona is coordinating a study involving more than a hundred experts to create a FAIR database of molecular simulations"},"content":{"rendered":"<p><strong><a href=\"https:\/\/www.pcb.ub.edu\/en\/empresa\/institut-de-recerca-biomedica-irb-barcelona\/\" target=\"_blank\" rel=\"noopener\">IRB Barcelona<\/a>, based at the Barcelona Science Park, has coordinated the publication of a study with more than a hundred experts in molecular simulation, advocating for a paradigm shift in the management of molecular dynamics data. The article, published in the journal Nature Methods, supports the implementation of FAIR principles (\u201cFindable, Accessible, Interoperable, Reusable\u201d) to enhance the reproducibility of calculations and facilitate their subsequent use as a source of information on the flexibility of biomacromolecules. The work, led by Dr. Modesto Orozco and Dr. Adam Hospital, proposes the creation of a common infrastructure to store and reuse data in the context of the AI revolution.<\/strong><\/p>\n<p>Unlike structural biology or genomics\u2014where data storage and sharing follow established common standards\u2014molecular simulation data remain fragmented and are often left forgotten on personal computers. This hinders the reproducibility of calculations and prevents their future reuse.<\/p>\n<p>The result is a formidable obstacle to integrating such data into the workflows of structural biology and biophysics, while also slowing the development of artificial intelligence (AI) methods, whose training relies heavily on access to vast amounts of dynamic data.<\/p>\n<p>In the article published in the journal <em>Nature Methods<\/em>, more than one hundred researchers raise awareness of this situation and advocate for a change of model: applying the FAIR principles\u2014which guarantee that the data are findable, accessible, interoperable, and reusable\u2014to simulation results. The article has been signed by renowned international experts, including two Nobel laureates and leading figures from the best research centres in the world. The proposed goal is to build an open and sustainable ecosystem that amplifies the impact of these data and avoids unnecessary duplication.<\/p>\n<p><iframe loading=\"lazy\" title=\"Towards a FAIR database for molecular simulations\" width=\"1080\" height=\"810\" src=\"https:\/\/www.youtube.com\/embed\/K8gAeL9VczY?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe><\/p>\n<h3><strong>\u201cReusing instead of repeating\u201d<\/strong><\/h3>\n<p>\u201cFor years, the community assumed that rerunning a simulation was easier and cheaper than archiving it. But that\u2019s no longer the case,&#8221; says <strong>Dr. Modesto Orozco<\/strong>, coordinator of the European project <a href=\"https:\/\/mddbr.eu\/\">MDDB<\/a>, head of the <a href=\"https:\/\/www.irbbarcelona.org\/en\/research\/molecular-modelling-and-bioinformatics\" target=\"_blank\" rel=\"noopener\">Molecular Modelling and Bioinformatics<\/a> lab at IRB Barcelona, Full Professor at the University of Barcelona and founder of the biotech Nostrum Biodiscovery.<\/p>\n<p>\u201cThe knowledge we can gain from reusing data is immense: it will allow us to identify new targets, train AI algorithms, and design new experiments,\u201d adds <strong>Dr. Adam Hospital<\/strong>. Both researchers lead the European Project MDDB (Molecular Dynamics Data Bank) \u2014funded by the Horizon Europe Programme run by the European Commission\u2014 which specifically aims to establish a centralized and accessible database for molecular simulations.<\/p>\n<h3><strong>Lessons from other fields<\/strong><\/h3>\n<p>The proposal draws inspiration from the success of other fields that have embraced open science. The Protein Data Bank, which has collected three-dimensional structures of biomacromolecules since the 1970s, has been instrumental\u2014not only in revealing the function of proteins and nucleic acids, enabling the &#8216;omics&#8217; revolution, and providing a holistic view of the cell, but also in the development of drugs, vaccines, and new therapies.<\/p>\n<p>The data stored there were key to training AlphaFold2, which was recognized with the 2024 Nobel Prize in Chemistry. The authors argue that complementing these structural data with dynamic information will open a new field whose developmental potential is difficult to grasp.<\/p>\n<p>According to the authors of the article, the time has come for the molecular simulation community to adopt practices similar to those of the structural and &#8216;omics&#8217; communities\u2014not only preserving data, but also standardizing file formats, metadata, and quality criteria. The text outlines how a federated infrastructure\u2014with distributed nodes and shared access tools\u2014could make this planet-scale archive feasible.<\/p>\n<h3><strong>Beyond storage<\/strong><\/h3>\n<p>The approach put forward in the article published in Nature Methods goes beyond merely storing data. It advocates for an integrated model\u2014from the precise documentation of simulations (including conditions, software, parameters, etc.) to their automated analysis, validation, and reuse through machine learning techniques. \u201cThe value of these data doesn\u2019t end with the publication of a paper or their presentation at a conference. Often, that\u2019s just the beginning,\u201d concludes <strong>Dr. Orozco<\/strong>. \u201cWe must treat data as a shared resource for science\u201d.<\/p>\n<p><strong>\u00bb Article of reference:<\/strong> The need to implement FAIR principles in biomolecular simulations. Rommie E. Amaro, Johan \u00c5qvist, (&#8230;) Adam Hospital, Modesto Orozco et al. Nature Methods (2025) doi: <a href=\"https:\/\/www.nature.com\/articles\/s41592-025-02635-0\" target=\"_blank\" rel=\"noopener\">10.1038\/s41592-025-02635-0<\/a><\/p>\n<p><strong>\u00bb Link to the news:<\/strong> <a href=\"https:\/\/www.irbbarcelona.org\/en\/news\/scientific\/towards-fair-database-molecular-simulations?utm_campaign=orozco-natmethods-apr25&amp;utm_content=en&amp;utm_medium=social&amp;utm_source=linkedin\" target=\"_blank\" rel=\"noopener\">web del IRB Barcelona [+]<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>IRB Barcelona, based at the Barcelona Science Park, has coordinated the publication of a study with more than a hundred experts in molecular simulation, advocating for a paradigm shift in&#8230;<\/p>\n","protected":false},"author":1,"featured_media":103742,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"categories":[36],"tags":[260],"class_list":["post-103748","post","type-post","status-publish","format-standard","has-post-thumbnail","category-science","tag-irb-en"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.4 - 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