{"id":49950,"date":"2015-11-17T00:00:00","date_gmt":"2015-11-16T23:00:00","guid":{"rendered":"http:\/\/www.pcb.ub.edu\/irb-barcelona-develops-an-advanced-method-and-the-first-platform-of-dna-simulations\/"},"modified":"2020-11-18T15:08:51","modified_gmt":"2020-11-18T14:08:51","slug":"irb-barcelona-develops-an-advanced-method-and-the-first-platform-of-dna-simulations","status":"publish","type":"post","link":"https:\/\/www.pcb.ub.edu\/en\/irb-barcelona-develops-an-advanced-method-and-the-first-platform-of-dna-simulations\/","title":{"rendered":"IRB Barcelona develops an advanced method and the first platform of DNA simulations"},"content":{"rendered":"<p>Seeing through simulations what is not possible to observe directly through experimental means. Molecular dynamics is a technique that allows the simulation of DNA movement, its folding into double, triple or quadruple strands, and even its interaction with proteins and drugs. Molecular dynamics is used to address the processes that occur over time scales ranging from picoseconds to minutes and it can be used for molecular systems of various sizes, from few nanometres to a meter.<\/p>\n<p>Headed by\u00a0Modesto Orozco,\u00a0the\u00a0<a href=\"http:\/\/www.irbbarcelona.org\/en\/research\/molecular-modelling-and-bioinformatics\" target=\"_blank\" rel=\"noopener noreferrer\">Molecular Modelling and Bioinformatics Lab\u00a0<\/a>at the Institute for Research in Biomedicine (IRB Barcelona) are developing several theoretical methods to better understand the behaviour of bio-macromolecules, in particular nucleic acids, on a wide spatial-temporal scale and with a focus on biomedical and biotech applications.<\/p>\n<p>Today the group has published a new model in\u00a0Nature Methods.\u00a0Developed in collaboration with the Barcelona SuperComputing Center (BSC) and laboratories in England and the US, this model allows atomic-level simulations of DNA dynamics and, to the great satisfaction of the researchers,\u201cwith extraordinary accuracy\u201d\u2014an achievement that has taken 5 years of work and the testing of more than 100 DNA systems.<\/p>\n<p>The data are stored in a public website that currently holds more than 4 Terabytes of information:\u00a0<a href=\"http:\/\/mmb.irbbarcelona.org\/ParmBSC1\/\" target=\"_blank\" rel=\"noopener noreferrer\">http:\/\/mmb.irbbarcelona.org\/ParmBSC1\/<\/a>. This web site is accessible through the Spanish Institute of Bioinformatics (INB) and the ELIXIR-Excellerate network, the largest collection of life sciences data in Europe, to which IRB Barcelona contributes.<\/p>\n<p>The scientists have developed what is called a force-field, a set of mathematical functions that describe the movement of the atoms that form DNA.\u00a0 \u201cA force-field has never previously allowed the study of such diverse structures in time scales relevant for understanding biological phenomena,\u201d assures\u00a0Pablo Dans Puiggr\u00f2s, IRB Barcelona researcher and first author of the paper, together with\u00a0Ivan Ivani, a PhD student in the same lab.<\/p>\n<p>In addition, the authors present the first online tool devoted to the simulation of nucleic acids, emphasizing that \u201cit allows to predict DNA properties, which can then be compared directly with experiments\u201d. \u201cWe hope that this new tool and method will open our work to a wider community of users\u201d says\u00a0Modesto Orozco, director of the project.<\/p>\n<p>The tool has potential applications in fields ranging from biomedicine to nanotechnology, providing information on mechanisms that underlie DNA regulation and contributing to improvements in the design of drugs that directly or indirectly target DNA. \u201cWe are achieving a quantitative leap in the quality of atomic DNA simulations,\u201d states\u00a0Pablo Dans Puiggr\u00f2s.<\/p>\n<p>\u201cAdvances in simulation are bringing us closer to the definition of a theoretical model that will allows us to simulate key aspects of cell life, therefore approaching the dream of being able to describe the behaviour of organisms only based on the basic rules of physics and chemistry,\u201d says\u00a0Modesto Orozco, who is also a senior professor at the University of Barcelona and director of the Life Sciences Department at BSC.<\/p>\n<p>The work, funded by the European Research council (ERC Advanced Grant), the Ministry of the Economy, the Government of Catalonia, and the Spanish Institute for Bioinformatics, is the result of collaboration between IRB Barcelona and BSC through a joint Computational Biology programme.<br \/>\n\u00a0<\/p>\n<p><strong>\u2022\u00a0Reference article:<\/strong><\/p>\n<p><em>Parmbsc1: as refined force-field for DNA simulations.<\/em> I\u00a0Ivani, P D. Dans, A Noy, A P\u00e9rez, I Faustino, A Hospital, J Walther, P Andrio, R Go\u00f1i, ABalaceanu, G Portella, F Battistini, J LlGelp\u00ed, C Gonz\u00e1lez, M Vendruscolo, C A. Laughton, S A. Harris, D A. Case,and M Orozco. Nature Methods\u00a0(2015). Doi:\u00a0<a href=\"http:\/\/www.nature.com\/nmeth\/journal\/vaop\/ncurrent\/full\/nmeth.3658.html\" target=\"_blank\" rel=\"noopener noreferrer\">10.1038\/nmeth.3658<\/a>.<\/p>\n<p>\u00a0<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The\u00a0Molecular Modelling and Bioinformatics Laboratory\u00a0at the Institute for Research in Biomedicine (<a href=\"http:\/\/www.pcb.ub.edu\/portal\/en\/cerca?p_p_id=cercador_WAR_empleatsempresesportlet&amp;p_p_lifecycle=0&amp;p_p_state=maximized&amp;p_p_mode=view&amp;p_p_col_id=column-1&amp;p_p_col_count=1&amp;_cercador_WAR_empleatsempresesportlet_jspPage=%2Fhtml%2Fcommon%2Fdetall-empresa.jsp&amp;_cercador_WAR_empleatsempresesportlet_empresaId=ENT_000001&amp;_cercador_WAR_empleatsempresesportlet_redirect=%2Fportal%2Fca%2Fcerca%3Fp_p_id%3Dcercador_WAR_empleatsempresesportlet%26p_p_lifecycle%3D0%26p_p_mode%3Dview%26_cercador_WAR_empleatsempresesportlet_tab%3D1%26_cercador_WAR_empleatsempresesportlet_keywords%3DIrb\" target=\"_blank\" rel=\"noopener noreferrer\">IRB Barcelona<\/a>),\u00a0headed by\u00a0Modesto Orozco,<a href=\"http:\/\/www.irbbarcelona.org\/en\/research\/molecular-modelling-and-bioinformatics\" target=\"_blank\" rel=\"noopener noreferrer\">\u00a0<\/a>has published today in\u00a0Nature Methods a new\u00a0model which allows\u00a0atomic-level simulations of DNA dynamics,\u00a0with unprecedented accuracy.\u00a0All the simulations and posterior analyses are kept in the first online tool developed to date dedicated to atomic level simulations of nucleic acids.\u00a0The platform is free of charge and available to the entire scientific community through the Spanish Institute of Bioinformatics and the European network <a href=\"https:\/\/www.elixir-europe.org\/news\/elixir-accelerates-major-horizon-2020-funding\" target=\"_blank\" rel=\"noopener noreferrer\">ELIXIR-Excellerate.<\/a><\/p>\n<p>\u00a0<\/p>\n","protected":false},"author":1,"featured_media":54801,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"categories":[8],"tags":[],"class_list":["post-49950","post","type-post","status-publish","format-standard","has-post-thumbnail","category-uncategorized"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - 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