{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T21:47:38Z","timestamp":1776289658095,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2021,5,13]],"date-time":"2021-05-13T00:00:00Z","timestamp":1620864000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100004727","name":"Flanders institute for biotechnology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004727","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Flanders Funds for Scientific Research Flanders","award":["I011220N"],"award-info":[{"award-number":["I011220N"]}]},{"name":"Flanders Funds for Scientific Research Flanders","award":["I011620N"],"award-info":[{"award-number":["I011620N"]}]},{"name":"Flanders Funds for Scientific Research Flanders","award":["G0H1716N"],"award-info":[{"award-number":["G0H1716N"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Proteins able to undergo liquid\u2013liquid phase separation (LLPS) in vivo and in vitro are drawing a lot of interest, due to their functional relevance for cell life. Nevertheless, the proteome-scale experimental screening of these proteins seems unfeasible, because besides being expensive and time-consuming, LLPS is heavily influenced by multiple environmental conditions such as concentration, pH and temperature, thus requiring a combinatorial number of experiments for each protein.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To overcome this problem, we propose a neural network model able to predict the LLPS behavior of proteins given specified experimental conditions, effectively predicting the outcome of in vitro experiments. Our model can be used to rapidly screen proteins and experimental conditions searching for LLPS, thus reducing the search space that needs to be covered experimentally. We experimentally validate Droppler\u2019s prediction on the TAR DNA-binding protein in different experimental conditions, showing the consistency of its predictions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>A python implementation of Droppler is available at https:\/\/bitbucket.org\/grogdrinker\/droppler<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab350","type":"journal-article","created":{"date-parts":[[2021,5,10]],"date-time":"2021-05-10T20:54:40Z","timestamp":1620680080000},"page":"3473-3479","source":"Crossref","is-referenced-by-count":29,"title":["<i>In silico<\/i> prediction of <i>in vitro<\/i> protein liquid\u2013liquid phase separation experiments outcomes with multi-head neural attention"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1157-1899","authenticated-orcid":false,"given":"Daniele","family":"Raimondi","sequence":"first","affiliation":[{"name":"ESAT-STADIUS, KU Leuven , 3001 Leuven, Belgium"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5935-5258","authenticated-orcid":false,"given":"Gabriele","family":"Orlando","sequence":"additional","affiliation":[{"name":"SWITCH Lab, Department of Cellular and Molecular Medicine, KU Leuven , 3001 Leuven, Belgium"}]},{"given":"Emiel","family":"Michiels","sequence":"additional","affiliation":[{"name":"SWITCH Lab, Department of Cellular and Molecular Medicine, KU Leuven , 3001 Leuven, Belgium"}]},{"given":"Donya","family":"Pakravan","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, LBI, KU Leuven , 3001 Leuven, Belgium"},{"name":"VIB, Center for Brain and Disease Research, Laboratory of Neurobiology , 3000 Leuven, Belgium"}]},{"given":"Anna","family":"Bratek-Skicki","sequence":"additional","affiliation":[{"name":"VIB-VUB Center for Structural Biology (CSB) , 1050 Brussels, Belgium"}]},{"given":"Ludo","family":"Van Den Bosch","sequence":"additional","affiliation":[{"name":"Department of Neurosciences, LBI, KU Leuven , 3001 Leuven, Belgium"},{"name":"VIB, Center for Brain and Disease Research, Laboratory of Neurobiology , 3000 Leuven, Belgium"}]},{"given":"Yves","family":"Moreau","sequence":"additional","affiliation":[{"name":"ESAT-STADIUS, KU Leuven , 3001 Leuven, Belgium"}]},{"given":"Frederic","family":"Rousseau","sequence":"additional","affiliation":[{"name":"SWITCH Lab, Department of Cellular and Molecular Medicine, KU Leuven , 3001 Leuven, Belgium"}]},{"given":"Joost","family":"Schymkowitz","sequence":"additional","affiliation":[{"name":"SWITCH Lab, Department of Cellular and Molecular Medicine, KU Leuven , 3001 Leuven, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2021,5,13]]},"reference":[{"key":"2023051609032588300_btab350-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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