{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T03:51:01Z","timestamp":1768017061466,"version":"3.49.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,5,21]],"date-time":"2020-05-21T00:00:00Z","timestamp":1590019200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["BFU2015-63571-P"],"award-info":[{"award-number":["BFU2015-63571-P"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Centro de Excelencia Severo Ochoa"},{"name":"Centres de Recerca de Catalunya (CERCA) Programme"},{"name":"\u2018la Caixa\u2019 Foundation","award":["LCF\/BQ\/DI19\/11730061"],"award-info":[{"award-number":["LCF\/BQ\/DI19\/11730061"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Accurate 3D modelling of protein\u2013protein interactions (PPI) is essential to compensate for the absence of experimentally determined complex structures. Here, we present a new set of commands within the ModelX toolsuite capable of generating atomic-level protein complexes suitable for interface design. Among these commands, the new tool ProteinFishing proposes known and\/or putative alternative 3D PPI for a given protein complex. The algorithm exploits backbone compatibility of protein fragments to generate mutually exclusive protein interfaces that are quickly evaluated with a knowledge-based statistical force field. Using interleukin-10-R2 co-crystalized with interferon-lambda-3, and a database of X-ray structures containing interleukin-10, this algorithm was able to generate interleukin-10-R2\/interleukin-10 structural models in agreement with experimental data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ProteinFishing is a portable command-line tool included in the ModelX toolsuite, written in C++, that makes use of an SQL (tested for MySQL and MariaDB) relational database delivered with a template SQL dump called FishXDB. FishXDB contains the empty tables of ModelX fragments and the data used by the embedded statistical force field. ProteinFishing is compiled for Linux-64bit, MacOS-64bit and Windows-32bit operating systems. This software is a proprietary license and is distributed as an executable with its correspondent database dumps. It can be downloaded publicly at http:\/\/modelx.crg.es\/. Licenses are freely available for academic users after registration on the website and are available under commercial license for for-profit organizations or companies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>javier.delgado@crg.eu or luis.serrano@crg.eu<\/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\/btaa533","type":"journal-article","created":{"date-parts":[[2020,5,18]],"date-time":"2020-05-18T19:52:35Z","timestamp":1589831555000},"page":"4208-4210","source":"Crossref","is-referenced-by-count":6,"title":["<i>ProteinFishing<\/i>: a protein complex generator within the ModelX toolsuite"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0702-2758","authenticated-orcid":false,"given":"Damiano","family":"Cianferoni","sequence":"first","affiliation":[{"name":"Systems Biology, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology , Barcelona 08003, Spain"}]},{"given":"Leandro G","family":"Radusky","sequence":"additional","affiliation":[{"name":"Systems Biology, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology , Barcelona 08003, Spain"}]},{"given":"Sarah A","family":"Head","sequence":"additional","affiliation":[{"name":"Systems Biology, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology , Barcelona 08003, Spain"}]},{"given":"Luis","family":"Serrano","sequence":"additional","affiliation":[{"name":"Systems Biology, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology , Barcelona 08003, Spain"},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona 08002, Spain"},{"name":"ICREA , Barcelona 08010, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1302-5445","authenticated-orcid":false,"given":"Javier","family":"Delgado","sequence":"additional","affiliation":[{"name":"Systems Biology, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology , Barcelona 08003, Spain"}]}],"member":"286","published-online":{"date-parts":[[2020,5,21]]},"reference":[{"key":"2023062213541072600_btaa533-B2639496","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023062213541072600_btaa533-B2","doi-asserted-by":"crossref","first-page":"3852","DOI":"10.1093\/nar\/gky228","article-title":"FoldX accurate structural protein\u2013DNA binding prediction using PADA1 (Protein Assisted DNA Assembly 1)","volume":"46","author":"Blanco","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023062213541072600_btaa533-B3","doi-asserted-by":"crossref","first-page":"24568","DOI":"10.1073\/pnas.1910999116","article-title":"Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX","volume":"116","author":"Delgado Blanco","year":"2019","journal-title":"Proc. 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