{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T10:18:31Z","timestamp":1777717111118,"version":"3.51.4"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2019,3,2]],"date-time":"2019-03-02T00:00:00Z","timestamp":1551484800000},"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\/501100003329","name":"Ministry of Economy and Competitiveness","doi-asserted-by":"publisher","award":["BIO2016 78310-R"],"award-info":[{"award-number":["BIO2016 78310-R"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Science Center","award":["MAESTRO2014\/14\/A\/ST6\/00088"],"award-info":[{"award-number":["MAESTRO2014\/14\/A\/ST6\/00088"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Aggrescan3D (A3D) standalone is a multiplatform Python package for structure-based prediction of protein aggregation properties and rational design of protein solubility. A3D allows the re-design of protein solubility by combining structural aggregation propensity and stability predictions, as demonstrated by a recent experimental study. It also enables predicting the impact of protein conformational fluctuations on the aggregation properties. The standalone A3D version is an upgrade of the original web server implementation\u2014it introduces a number of customizable options, automated analysis of multiple mutations and offers a flexible computational framework for merging it with other computational tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>A3D standalone is distributed under the MIT license, which is free for academic and non-profit users. It is implemented in Python. The A3D standalone source code, wiki with documentation and examples of use, and installation instructions for Linux, macOS and Windows are available in the A3D standalone repository at https:\/\/bitbucket.org\/lcbio\/aggrescan3d.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz143","type":"journal-article","created":{"date-parts":[[2019,2,27]],"date-time":"2019-02-27T12:45:02Z","timestamp":1551271502000},"page":"3834-3835","source":"Crossref","is-referenced-by-count":36,"title":["Aggrescan3D standalone package for structure-based prediction of protein aggregation properties"],"prefix":"10.1093","volume":"35","author":[{"given":"Aleksander","family":"Kuriata","sequence":"first","affiliation":[{"name":"Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentin","family":"Iglesias","sequence":"additional","affiliation":[{"name":"Institut de Biotecnologia i de Biomedicina and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mateusz","family":"Kurcinski","sequence":"additional","affiliation":[{"name":"Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Salvador","family":"Ventura","sequence":"additional","affiliation":[{"name":"Institut de Biotecnologia i de Biomedicina and Departament de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona, Barcelona, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7623-0935","authenticated-orcid":false,"given":"Sebastian","family":"Kmiecik","sequence":"additional","affiliation":[{"name":"Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,3,2]]},"reference":[{"key":"2023013108194216600_btz143-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.csbj.2018.01.002","article-title":"FoldX as protein engineering tool: better than random based approaches?","volume":"16","author":"Bu\u00df","year":"2018","journal-title":"Comput. 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