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category-training category-career-development category-research tag-phase-separation tag-protein-aggregation tag-training-school tag-young-researchers"> <header class="entry-header"> <h1 class="entry-title">A Journey through Databases and Computational Tools on Phase Separation</h1> <div class="entry-meta"> <span class="posted-on">Posted on <a href="https://phasage.eu/a-journey-through-databases-and-computational-tools-on-phase-separation/" rel="bookmark"><time class="entry-date published" datetime="2024-03-07T10:13:02+00:00">March 7, 2024</time><time class="updated hide" datetime="2024-03-14T14:38:00+00:00">March 14, 2024</time></a></span><span class="byline"> by <span class="author vcard"><a rel="author" class="url fn n" href="https://phasage.eu/author/rvilaca/">Rita Vilaça</a></span></span> </div> </header> <div class="entry-content"> <div data-elementor-type="wp-post" data-elementor-id="10622" class="elementor elementor-10622"> <section class="elementor-section elementor-top-section elementor-element elementor-element-d8e9d0e elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="d8e9d0e" data-element_type="section"> <div class="elementor-container elementor-column-gap-default"> <div class="elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-40ea699" data-id="40ea699" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-f2b56ed elementor-widget elementor-widget-text-editor" data-id="f2b56ed" data-element_type="widget" data-widget_type="text-editor.default"> <div class="elementor-widget-container"> <p>By Sofia Figueiredo, Luis Fernando Durán Armenta and Rita Vilaça</p> </div> </div> </div> </div> </div> </section> <section class="elementor-section elementor-top-section elementor-element elementor-element-3b404b4 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="3b404b4" data-element_type="section"> <div class="elementor-container elementor-column-gap-default"> <div class="elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-b130535" data-id="b130535" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-9ab84e2 elementor-widget elementor-widget-text-editor" data-id="9ab84e2" data-element_type="widget" data-widget_type="text-editor.default"> <div class="elementor-widget-container"> <p>One week ago, we hosted the fifth edition of the <a href="https://phasage.eu/training-school-5/">PhasAGE Training School</a> which took place at the Vrije Universiteit Brussel (VUB), part of the Vlaams Instituut voor Biotechnologie (VIB). The event was organized by Peter Tompa, one of the core team members of the PhasAGE project, and his <a href="https://tompalab.sites.vib.be/en" target="_blank" rel="noopener">research group</a>.</p> </div> </div> <div class="elementor-element elementor-element-67efac9 elementor-widget elementor-widget-text-editor" data-id="67efac9" data-element_type="widget" data-widget_type="text-editor.default"> <div class="elementor-widget-container"> <p>The focus of this Training School was to explore advances and applications of Databases and Computational Tools on Phase Separation. The selected participants, mainly PhD candidates, received multidisciplinary training to gain practical experience in applying databases, in silico resources, and computational tools to query relevant biological data and analyse it in context.</p> </div> </div> </div> </div> </div> </section> <section class="elementor-section elementor-top-section elementor-element elementor-element-d1c9d1e elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="d1c9d1e" data-element_type="section"> <div class="elementor-container elementor-column-gap-default"> <div class="elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-d6f07b4" data-id="d6f07b4" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-1e2d4cf elementor-widget elementor-widget-text-editor" data-id="1e2d4cf" data-element_type="widget" data-widget_type="text-editor.default"> <div class="elementor-widget-container"> <p>The <a href="https://phasage.eu/training-school-5/">scientific program</a> included both theoretical and practical lessons by leading experts in the fields of LLPS, IDPs, and aggregation. </p><p>Our invited speakers and trainers come from reknown institutions from within and beyond the PhasAGE consortium. </p><p>During the practical sessions, participants were divided into groups and immersed in hands-on activities aimed at understanding the intricate details of proteins such as tau protein, TDP-43, ataxin-3, and a-synuclein. Each group was assigned with a specific protein to further explore their biological significance, their relevance in disease processes, and the potential for therapeutic targeting, focusing on their capacity to undergo phase separation and/or aggregation.</p> </div> </div> </div> </div> <div class="elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-d428f37" data-id="d428f37" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-cbf3409 elementor-widget elementor-widget-image" data-id="cbf3409" data-element_type="widget" data-widget_type="image.default"> <div class="elementor-widget-container"> <figure class="wp-caption"> <img fetchpriority="high" decoding="async" width="800" height="450" src="https://phasage.eu/wp-content/uploads/2024/03/opening-session-1024x576.jpg" class="attachment-large size-large wp-image-10643" alt="" srcset="https://phasage.eu/wp-content/uploads/2024/03/opening-session-1024x576.jpg 1024w, https://phasage.eu/wp-content/uploads/2024/03/opening-session-300x169.jpg 300w, https://phasage.eu/wp-content/uploads/2024/03/opening-session-768x432.jpg 768w, https://phasage.eu/wp-content/uploads/2024/03/opening-session-1536x864.jpg 1536w, https://phasage.eu/wp-content/uploads/2024/03/opening-session-2048x1152.jpg 2048w" sizes="(max-width: 800px) 100vw, 800px" /> <figcaption class="widget-image-caption wp-caption-text">Participants at the opening session of the PhasAEG Training School at VIB.</figcaption> </figure> </div> </div> </div> </div> </div> </section> <section class="elementor-section elementor-top-section elementor-element elementor-element-292e825 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="292e825" data-element_type="section"> <div class="elementor-container elementor-column-gap-default"> <div class="elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-5815fe7" data-id="5815fe7" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-fa619d1 elementor-widget elementor-widget-text-editor" data-id="fa619d1" data-element_type="widget" data-widget_type="text-editor.default"> <div class="elementor-widget-container"> <p>Trainees applied several bioinformatics tools and databases to analyze protein structure and predict functional characteristics for their assigned protein models, including Tango, Waltz, AggreScan, PASTA, BetaScan, PyMol, ChimeraX, and CIDER-kappa, among others. Specific tools tailored for intrinsically disordered proteins (IDPs) and LLPS were also explored to gain deeper insights into the behavior of the proteins.</p> </div> </div> </div> </div> </div> </section> <section class="elementor-section elementor-top-section elementor-element elementor-element-e5a2d27 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="e5a2d27" data-element_type="section"> <div class="elementor-container elementor-column-gap-default"> <div class="elementor-column elementor-col-33 elementor-top-column elementor-element elementor-element-9f0348e" data-id="9f0348e" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-d09615a elementor-widget elementor-widget-image" data-id="d09615a" data-element_type="widget" data-widget_type="image.default"> <div class="elementor-widget-container"> <figure class="wp-caption"> <img decoding="async" width="800" height="534" src="https://phasage.eu/wp-content/uploads/2024/03/Training-1-1-1024x683.jpg" class="attachment-large size-large wp-image-10644" alt="" srcset="https://phasage.eu/wp-content/uploads/2024/03/Training-1-1-1024x683.jpg 1024w, https://phasage.eu/wp-content/uploads/2024/03/Training-1-1-300x200.jpg 300w, https://phasage.eu/wp-content/uploads/2024/03/Training-1-1-768x512.jpg 768w, https://phasage.eu/wp-content/uploads/2024/03/Training-1-1.jpg 1381w" sizes="(max-width: 800px) 100vw, 800px" /> <figcaption class="widget-image-caption wp-caption-text">Trainees working in groups during the practical sessions.</figcaption> </figure> </div> </div> </div> </div> <div class="elementor-column elementor-col-33 elementor-top-column elementor-element elementor-element-18a415a" data-id="18a415a" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-8e13c98 elementor-widget elementor-widget-image" data-id="8e13c98" data-element_type="widget" data-widget_type="image.default"> <div class="elementor-widget-container"> <img loading="lazy" decoding="async" width="800" height="533" src="https://phasage.eu/wp-content/uploads/2024/03/Training-3-1.jpg" class="attachment-large size-large wp-image-10645" alt="" srcset="https://phasage.eu/wp-content/uploads/2024/03/Training-3-1.jpg 921w, https://phasage.eu/wp-content/uploads/2024/03/Training-3-1-300x200.jpg 300w, https://phasage.eu/wp-content/uploads/2024/03/Training-3-1-768x512.jpg 768w" sizes="(max-width: 800px) 100vw, 800px" /> </div> </div> </div> </div> <div class="elementor-column elementor-col-33 elementor-top-column elementor-element elementor-element-45a93fe" data-id="45a93fe" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-8fb48d6 elementor-widget elementor-widget-image" data-id="8fb48d6" data-element_type="widget" data-widget_type="image.default"> <div class="elementor-widget-container"> <img loading="lazy" decoding="async" width="800" height="534" src="https://phasage.eu/wp-content/uploads/2024/03/Training-2-1-1024x683.jpg" class="attachment-large size-large wp-image-10646" alt="" srcset="https://phasage.eu/wp-content/uploads/2024/03/Training-2-1-1024x683.jpg 1024w, https://phasage.eu/wp-content/uploads/2024/03/Training-2-1-300x200.jpg 300w, https://phasage.eu/wp-content/uploads/2024/03/Training-2-1-768x512.jpg 768w, https://phasage.eu/wp-content/uploads/2024/03/Training-2-1.jpg 1381w" sizes="(max-width: 800px) 100vw, 800px" /> </div> </div> </div> </div> </div> </section> <section class="elementor-section elementor-top-section elementor-element elementor-element-ce270f7 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="ce270f7" data-element_type="section"> <div class="elementor-container elementor-column-gap-default"> <div class="elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-2c5d923" data-id="2c5d923" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-d09f7e6 elementor-widget elementor-widget-text-editor" data-id="d09f7e6" data-element_type="widget" data-widget_type="text-editor.default"> <div class="elementor-widget-container"> <p>The participants also contributed to the scientific program with group presentations of their case studies. There is no better way to break the ice than a scientific discussion with Belgian beers and fries! The PhasAGE-VIB Training School also allowed the participants, the trainers, and the speakers to network and socialize during the introductory activity, the coffee breaks, at lunch, and of course, the social dinner with delicious Belgian specialities! This was a great opportunity to relax, meet old friends from previous editions of our events and make new ones.</p> </div> </div> </div> </div> </div> </section> <section class="elementor-section elementor-top-section elementor-element elementor-element-ffac616 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="ffac616" data-element_type="section"> <div class="elementor-container elementor-column-gap-default"> <div class="elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-51e4106" data-id="51e4106" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-7d9feca elementor-widget elementor-widget-image" data-id="7d9feca" data-element_type="widget" data-widget_type="image.default"> <div class="elementor-widget-container"> <figure class="wp-caption"> <img loading="lazy" decoding="async" width="800" height="600" src="https://phasage.eu/wp-content/uploads/2024/03/20240228_101958-1-1024x768.jpg" class="attachment-large size-large wp-image-10647" alt="" srcset="https://phasage.eu/wp-content/uploads/2024/03/20240228_101958-1-1024x768.jpg 1024w, https://phasage.eu/wp-content/uploads/2024/03/20240228_101958-1-300x225.jpg 300w, https://phasage.eu/wp-content/uploads/2024/03/20240228_101958-1-768x576.jpg 768w, https://phasage.eu/wp-content/uploads/2024/03/20240228_101958-1-1536x1152.jpg 1536w, https://phasage.eu/wp-content/uploads/2024/03/20240228_101958-1-2048x1536.jpg 2048w" sizes="(max-width: 800px) 100vw, 800px" /> <figcaption class="widget-image-caption wp-caption-text">Group photo with participants and organizing team at VIB and at social event. </figcaption> </figure> </div> </div> </div> </div> <div class="elementor-column elementor-col-50 elementor-top-column elementor-element elementor-element-9745f1c" data-id="9745f1c" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-dbca286 elementor-widget elementor-widget-image" data-id="dbca286" data-element_type="widget" data-widget_type="image.default"> <div class="elementor-widget-container"> <img loading="lazy" decoding="async" width="800" height="600" src="https://phasage.eu/wp-content/uploads/2024/03/20240227_200400-1-1024x768.jpg" class="attachment-large size-large wp-image-10648" alt="" srcset="https://phasage.eu/wp-content/uploads/2024/03/20240227_200400-1-1024x768.jpg 1024w, https://phasage.eu/wp-content/uploads/2024/03/20240227_200400-1-300x225.jpg 300w, https://phasage.eu/wp-content/uploads/2024/03/20240227_200400-1-768x576.jpg 768w, https://phasage.eu/wp-content/uploads/2024/03/20240227_200400-1-1536x1152.jpg 1536w, https://phasage.eu/wp-content/uploads/2024/03/20240227_200400-1-2048x1536.jpg 2048w" sizes="(max-width: 800px) 100vw, 800px" /> </div> </div> </div> </div> </div> </section> <section class="elementor-section elementor-top-section elementor-element elementor-element-ec5ec95 elementor-section-boxed elementor-section-height-default elementor-section-height-default" data-id="ec5ec95" data-element_type="section"> <div class="elementor-container elementor-column-gap-default"> <div class="elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-6d0340a" data-id="6d0340a" data-element_type="column"> <div class="elementor-widget-wrap elementor-element-populated"> <div class="elementor-element elementor-element-bd511a7 elementor-widget elementor-widget-text-editor" data-id="bd511a7" data-element_type="widget" data-widget_type="text-editor.default"> <div class="elementor-widget-container"> <p>At the end, the overall training school provided trainees with invaluable hands-on experience in bioinformatics analyses, fostering a deeper understanding of protein structure and function. By integrating theoretical knowledge with guided exploration, participants are now equipped to navigate the complexities of their proteins of interest and explore avenues for therapeutic intervention.</p><p>Thank you all for attending another successful edition!</p><p>Hartelijk dank!</p> </div> </div> </div> </div> </div> </section> </div> </div> <footer class="entry-footer"><span class="cat-links">Posted in <a href="https://phasage.eu/category/training/" rel="category tag">training</a>, <a href="https://phasage.eu/category/career-development/" rel="category tag">career development</a>, <a href="https://phasage.eu/category/research/" rel="category tag">research</a></span><span class="tags-links">Tagged <a href="https://phasage.eu/tag/phase-separation/" rel="tag">phase separation</a>, <a href="https://phasage.eu/tag/protein-aggregation/" rel="tag">protein aggregation</a>, <a href="https://phasage.eu/tag/training-school/" rel="tag">training school</a>, <a href="https://phasage.eu/tag/young-researchers/" rel="tag">young researchers</a></span></footer> </article> </main> </div> </div> </div> <footer id="colophon" class="site-footer" role="contentinfo"> <div id="footer-widgets" class="footer-widgets section-padding "> <div class="container"> <div class="row"> <div id="footer-1" class="col-md-6 col-sm-12 footer-column widget-area sidebar" role="complementary"> <aside id="text-7" class="footer-widget widget widget_text"><h2 class="widget-title">CONTACT</h2> <div class="textwidget"><p>phasageproject@i3s.up.pt</p> </div> </aside><aside id="media_image-9" class="footer-widget widget widget_media_image"><h2 class="widget-title">FOLLOW US:</h2><a href="https://twitter.com/PhasAGE_project"><img width="30" height="30" src="https://phasage.eu/wp-content/uploads/2023/08/Design-sem-nome.png" class="image wp-image-9607 attachment-30x30 size-30x30" alt="" style="max-width: 100%; height: auto;" title="FOLLOW US:" decoding="async" /></a></aside> </div> <div id="footer-2" class="col-md-6 col-sm-12 footer-column widget-area sidebar" role="complementary"> <aside id="media_image-7" class="footer-widget widget widget_media_image"><a href="https://cordis.europa.eu/project/id/952334"><img width="3377" height="912" src="https://phasage.eu/wp-content/uploads/2021/02/fundingflag_white.png" class="image wp-image-1517 attachment-full size-full" alt="" style="max-width: 100%; height: auto;" decoding="async" srcset="https://phasage.eu/wp-content/uploads/2021/02/fundingflag_white.png 3377w, https://phasage.eu/wp-content/uploads/2021/02/fundingflag_white-300x81.png 300w, https://phasage.eu/wp-content/uploads/2021/02/fundingflag_white-1024x277.png 1024w, https://phasage.eu/wp-content/uploads/2021/02/fundingflag_white-768x207.png 768w, https://phasage.eu/wp-content/uploads/2021/02/fundingflag_white-1536x415.png 1536w, https://phasage.eu/wp-content/uploads/2021/02/fundingflag_white-2048x553.png 2048w" sizes="(max-width: 3377px) 100vw, 3377px" /></a></aside><aside id="text-5" class="footer-widget widget widget_text"><h2 class="widget-title">Disclaimer</h2> <div class="textwidget"><p>“The content of this website only represents the views of the authors and cannot be considered to reflect the views of the European Commission, which is free of any responsibility for the use of the information contained herein.”</p> </div> </aside> </div> </div> </div> </div> <div class="site-info"> <div class="container"> <div class="btt"> <a class="back-to-top" href="#page" title="Back To Top"><i class="fa fa-angle-double-up wow flash" data-wow-duration="2s"></i></a> </div> Copyright © 2024 PhasAGE <span class="sep"> – </span> <a href="https://www.famethemes.com/themes/onepress">OnePress</a> theme by FameThemes </div> </div> </footer> </div> <script> ( function ( body ) { 'use strict'; body.className = body.className.replace( /\btribe-no-js\b/, 'tribe-js' ); } )( document.body ); </script> <script> /* <![CDATA[ */var tribe_l10n_datatables = {"aria":{"sort_ascending":": activate to sort column ascending","sort_descending":": activate to sort column descending"},"length_menu":"Show _MENU_ entries","empty_table":"No data available in table","info":"Showing _START_ to _END_ of _TOTAL_ entries","info_empty":"Showing 0 to 0 of 0 entries","info_filtered":"(filtered from _MAX_ total entries)","zero_records":"No matching records found","search":"Search:","all_selected_text":"All items on this page were selected. 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