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</div> <div class="control"> <button class="button is-small is-link">Go</button> </div> </div> </form> </div> </div> <ol class="breathe-horizontal" start="1"> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2305.15453">arXiv:2305.15453</a> <span> [<a href="https://arxiv.org/pdf/2305.15453">pdf</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Quantitative Methods">q-bio.QM</span> </div> </div> <p class="title is-5 mathjax"> Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Maier%2C+A">Andreas Maier</a>, <a href="/search/q-bio?searchtype=author&query=Hartung%2C+M">Michael Hartung</a>, <a href="/search/q-bio?searchtype=author&query=Abovsky%2C+M">Mark Abovsky</a>, <a href="/search/q-bio?searchtype=author&query=Adamowicz%2C+K">Klaudia Adamowicz</a>, <a href="/search/q-bio?searchtype=author&query=Bader%2C+G+D">Gary D. Bader</a>, <a href="/search/q-bio?searchtype=author&query=Baier%2C+S">Sylvie Baier</a>, <a href="/search/q-bio?searchtype=author&query=Blumenthal%2C+D+B">David B. Blumenthal</a>, <a href="/search/q-bio?searchtype=author&query=Chen%2C+J">Jing Chen</a>, <a href="/search/q-bio?searchtype=author&query=Elkjaer%2C+M+L">Maria L. Elkjaer</a>, <a href="/search/q-bio?searchtype=author&query=Garcia-Hernandez%2C+C">Carlos Garcia-Hernandez</a>, <a href="/search/q-bio?searchtype=author&query=Helmy%2C+M">Mohamed Helmy</a>, <a href="/search/q-bio?searchtype=author&query=Hoffmann%2C+M">Markus Hoffmann</a>, <a href="/search/q-bio?searchtype=author&query=Jurisica%2C+I">Igor Jurisica</a>, <a href="/search/q-bio?searchtype=author&query=Kotlyar%2C+M">Max Kotlyar</a>, <a href="/search/q-bio?searchtype=author&query=Lazareva%2C+O">Olga Lazareva</a>, <a href="/search/q-bio?searchtype=author&query=Levi%2C+H">Hagai Levi</a>, <a href="/search/q-bio?searchtype=author&query=List%2C+M">Markus List</a>, <a href="/search/q-bio?searchtype=author&query=Lobentanzer%2C+S">Sebastian Lobentanzer</a>, <a href="/search/q-bio?searchtype=author&query=Loscalzo%2C+J">Joseph Loscalzo</a>, <a href="/search/q-bio?searchtype=author&query=Malod-Dognin%2C+N">Noel Malod-Dognin</a>, <a href="/search/q-bio?searchtype=author&query=Manz%2C+Q">Quirin Manz</a>, <a href="/search/q-bio?searchtype=author&query=Matschinske%2C+J">Julian Matschinske</a>, <a href="/search/q-bio?searchtype=author&query=Mee%2C+M">Miles Mee</a>, <a href="/search/q-bio?searchtype=author&query=Oubounyt%2C+M">Mhaned Oubounyt</a>, <a href="/search/q-bio?searchtype=author&query=Pico%2C+A+R">Alexander R. Pico</a> , et al. (14 additional authors not shown) </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2305.15453v2-abstract-short" style="display: inline;"> In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2305.15453v2-abstract-full').style.display = 'inline'; document.getElementById('2305.15453v2-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2305.15453v2-abstract-full" style="display: none;"> In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network medicine tools have emerged to identify potential drug repurposing candidates. However, these tools often require complex installation and lack intuitive visual network mining capabilities. To tackle these challenges, we introduce Drugst.One, a platform that assists specialized computational medicine tools in becoming user-friendly, web-based utilities for drug repurposing. With just three lines of code, Drugst.One turns any systems biology software into an interactive web tool for modeling and analyzing complex protein-drug-disease networks. Demonstrating its broad adaptability, Drugst.One has been successfully integrated with 21 computational systems medicine tools. Available at https://drugst.one, Drugst.One has significant potential for streamlining the drug discovery process, allowing researchers to focus on essential aspects of pharmaceutical treatment research. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2305.15453v2-abstract-full').style.display = 'none'; document.getElementById('2305.15453v2-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 4 July, 2023; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 24 May, 2023; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> May 2023. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">45 pages, 6 figures, 7 tables</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2004.12420">arXiv:2004.12420</a> <span> [<a href="https://arxiv.org/pdf/2004.12420">pdf</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Molecular Networks">q-bio.MN</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1038/s41467-020-17189-2">10.1038/s41467-020-17189-2 <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Sadegh%2C+S">Sepideh Sadegh</a>, <a href="/search/q-bio?searchtype=author&query=Matschinske%2C+J">Julian Matschinske</a>, <a href="/search/q-bio?searchtype=author&query=Blumenthal%2C+D+B">David B. Blumenthal</a>, <a href="/search/q-bio?searchtype=author&query=Galindez%2C+G">Gihanna Galindez</a>, <a href="/search/q-bio?searchtype=author&query=Kacprowski%2C+T">Tim Kacprowski</a>, <a href="/search/q-bio?searchtype=author&query=List%2C+M">Markus List</a>, <a href="/search/q-bio?searchtype=author&query=Nasirigerdeh%2C+R">Reza Nasirigerdeh</a>, <a href="/search/q-bio?searchtype=author&query=Oubounyt%2C+M">Mhaned Oubounyt</a>, <a href="/search/q-bio?searchtype=author&query=Pichlmair%2C+A">Andreas Pichlmair</a>, <a href="/search/q-bio?searchtype=author&query=Rose%2C+T+D">Tim Daniel Rose</a>, <a href="/search/q-bio?searchtype=author&query=Salgado-Albarr%C3%A1n%2C+M">Marisol Salgado-Albarr谩n</a>, <a href="/search/q-bio?searchtype=author&query=Sp%C3%A4th%2C+J">Julian Sp盲th</a>, <a href="/search/q-bio?searchtype=author&query=Stukalov%2C+A">Alexey Stukalov</a>, <a href="/search/q-bio?searchtype=author&query=Wenke%2C+N+K">Nina K. Wenke</a>, <a href="/search/q-bio?searchtype=author&query=Yuan%2C+K">Kevin Yuan</a>, <a href="/search/q-bio?searchtype=author&query=Pauling%2C+J+K">Josch K. Pauling</a>, <a href="/search/q-bio?searchtype=author&query=Baumbach%2C+J">Jan Baumbach</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2004.12420v1-abstract-short" style="display: inline;"> Coronavirus Disease-2019 (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus. It was first identified in Wuhan, China, and has since spread causing a global pandemic. Various studies have been performed to understand the molecular mechanisms of viral infection for predicting drug repurposing candidates. However, such information is spread across many publications and it is very time… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2004.12420v1-abstract-full').style.display = 'inline'; document.getElementById('2004.12420v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2004.12420v1-abstract-full" style="display: none;"> Coronavirus Disease-2019 (COVID-19) is an infectious disease caused by the SARS-CoV-2 virus. It was first identified in Wuhan, China, and has since spread causing a global pandemic. Various studies have been performed to understand the molecular mechanisms of viral infection for predicting drug repurposing candidates. However, such information is spread across many publications and it is very time-consuming to access, integrate, explore, and exploit. We developed CoVex, the first interactive online platform for SARS-CoV-2 and SARS-CoV-1 host interactome exploration and drug (target) identification. CoVex integrates 1) experimentally validated virus-human protein interactions, 2) human protein-protein interactions and 3) drug-target interactions. The web interface allows user-friendly visual exploration of the virus-host interactome and implements systems medicine algorithms for network-based prediction of drugs. Thus, CoVex is an important resource, not only to understand the molecular mechanisms involved in SARS-CoV-2 and SARS-CoV-1 pathogenicity, but also in clinical research for the identification and prioritization of candidate therapeutics. We apply CoVex to investigate recent hypotheses on a systems biology level and to systematically explore the molecular mechanisms driving the virus life cycle. Furthermore, we extract and discuss drug repurposing candidates involved in these mechanisms. CoVex renders COVID-19 drug research systems-medicine-ready by giving the scientific community direct access to network medicine algorithms integrating virus-host-drug interactions. It is available at https://exbio.wzw.tum.de/covex/. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2004.12420v1-abstract-full').style.display = 'none'; document.getElementById('2004.12420v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 26 April, 2020; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> April 2020. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">15 pages, 4 figures</span> </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> Nat Commun 11, 3518 (2020) </p> </li> </ol> <div class="is-hidden-tablet">  <span class="help" style="display: inline-block;"><a href="https://github.com/arXiv/arxiv-search/releases">Search v0.5.6 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