{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T16:46:04Z","timestamp":1775666764934,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2025,7,26]],"date-time":"2025-07-26T00:00:00Z","timestamp":1753488000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Research Council of Finland for financial support","award":["358505"],"award-info":[{"award-number":["358505"]}]},{"name":"Research Council of Finland for financial support","award":["356568"],"award-info":[{"award-number":["356568"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Finding proteins with specific functions by mining modern databases can potentially lead to substantial advancements in wide range of fields, from medicine and biotechnology to material science. Currently available algorithms enable mining of proteins based on their sequence or structure. However, activities of many proteins, such as enzymes and drug targets, are dictated by active site residues and their surroundings rather than the overall structure or sequence of a protein.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce ActSeek\u2014a computer vision-inspired fast program\u2014that searches structural databases for proteins with active sites similar to the seed protein. ActSeek is implemented to mine proteins with desired active site environments from the Alphafold database. The potential of ActSeek to find innovative solutions to the world\u2019s most pressing challenges is demonstrated by finding enzymes that may be used to produce biodegradable plastics or degrade plastics, as well as potential off-targets for common drug molecules.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>ActSeek source code is available in https:\/\/github.com\/vttresearch\/ActSeek under Non-Commercial License Agreement.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf424","type":"journal-article","created":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T11:55:26Z","timestamp":1753271726000},"source":"Crossref","is-referenced-by-count":1,"title":["ActSeek: fast and accurate search algorithm of active sites in alphafold database"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1968-4820","authenticated-orcid":false,"given":"Sandra","family":"Castillo","sequence":"first","affiliation":[{"name":"VTT Technical Research Centre of Finland Ltd , Espoo, Otaniemi, 02044 VTT,","place":["Finland"]}]},{"given":"Osmo Henri Samuli","family":"Ollila","sequence":"additional","affiliation":[{"name":"VTT Technical Research Centre of Finland Ltd , Espoo, Otaniemi, 02044 VTT,","place":["Finland"]}]}],"member":"286","published-online":{"date-parts":[[2025,7,26]]},"reference":[{"key":"2025081319160885500_btaf424-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 Mol Biol"},{"key":"2025081319160885500_btaf424-B2","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1109\/TPAMI.1987.4767965","article-title":"Least-squares fitting of two 3-d point sets","author":"Arun","year":"1987","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"key":"2025081319160885500_btaf424-B3","doi-asserted-by":"crossref","first-page":"vi35","DOI":"10.1093\/annonc\/mdm222","article-title":"Erlotinib in cancer treatment","volume":"18","author":"Bareschino","year":"2007","journal-title":"Annal Oncol"},{"key":"2025081319160885500_btaf424-B4","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":"Nucl Acids Res"},{"key":"2025081319160885500_btaf424-B5","doi-asserted-by":"crossref","first-page":"e1008502","DOI":"10.1371\/journal.pcbi.1008502","article-title":"Real-time structural motif searching in proteins using an inverted index strategy","volume":"16","author":"Bittrich","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2025081319160885500_btaf424-B6","doi-asserted-by":"crossref","first-page":"2170","DOI":"10.1182\/blood-2007-07-100362","article-title":"Erlotinib exhibits antineoplastic off-target effects in AML and MDS: a preclinical study","volume":"111","author":"Boehrer","year":"2008","journal-title":"Blood"},{"key":"2025081319160885500_btaf424-B7","doi-asserted-by":"crossref","first-page":"D564","DOI":"10.1093\/nar\/gkae1091","article-title":"Updated resources for exploring experimentally-determined pdb structures and computed structure models at the rcsb protein data bank","volume":"53","author":"Burley","year":"2025","journal-title":"Nucl Acids Res"},{"key":"2025081319160885500_btaf424-B8","unstructured":"Castillo S, Ollila S. \u00a02025. 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