{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T21:53:44Z","timestamp":1775080424433,"version":"3.50.1"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2023,10,25]],"date-time":"2023-10-25T00:00:00Z","timestamp":1698192000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Italian Capacity for Structural Biology Services in Instruct-ERIC"},{"name":"European Union\u2014NextGenerationEU and EOSC-Life"},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["824087"],"award-info":[{"award-number":["824087"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>In recent years, high-throughput sequencing technologies have made available the genome sequences of a huge variety of organisms. However, the functional annotation of the encoded proteins often still relies on low-throughput and costly experimental studies. Bioinformatics approaches offer a promising alternative to accelerate this process. In this work, we focus on the binding of zinc(II) ions, which is needed for 5%\u201310% of any organism\u2019s proteins to achieve their physiologically relevant form.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To implement a predictor of zinc(II)-binding sites in the 3D structures of proteins, we used a neural network, followed by a filter of the network output against the local structure of all known sites. The latter was implemented as a function comparing the distance matrices of the C\u03b1 and C\u03b2 atoms of the sites. We called the resulting tool Master of Metals (MOM). The structural models for the entire proteome of an organism generated by AlphaFold can be used as input to our tool in order to achieve annotation at the whole organism level within a few hours. To demonstrate this, we applied MOM to the yeast proteome, obtaining a precision of about 76%, based on data for homologous proteins.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Master of Metals has been implemented in Python and is available at https:\/\/github.com\/cerm-cirmmp\/Master-of-metals.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad653","type":"journal-article","created":{"date-parts":[[2023,10,25]],"date-time":"2023-10-25T19:02:02Z","timestamp":1698260522000},"source":"Crossref","is-referenced-by-count":13,"title":["Hunting down zinc(II)-binding sites in proteins with distance matrices"],"prefix":"10.1093","volume":"39","author":[{"given":"Vincenzo","family":"Laveglia","sequence":"first","affiliation":[{"name":"Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy"}]},{"given":"Milana","family":"Bazayeva","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy"},{"name":"Magnetic Resonance Center (CERM), University of Florence , Sesto Fiorentino 50019, Italy"}]},{"given":"Claudia","family":"Andreini","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy"},{"name":"Magnetic Resonance Center (CERM), University of Florence , Sesto Fiorentino 50019, Italy"},{"name":"Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine , Sesto Fiorentino 50019, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6172-0368","authenticated-orcid":false,"given":"Antonio","family":"Rosato","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Florence , Sesto Fiorentino 50019, Italy"},{"name":"Magnetic Resonance Center (CERM), University of Florence , Sesto Fiorentino 50019, Italy"},{"name":"Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine , Sesto Fiorentino 50019, Italy"}]}],"member":"286","published-online":{"date-parts":[[2023,10,25]]},"reference":[{"key":"2023110804053531000_btad653-B1","doi-asserted-by":"crossref","first-page":"e26325","DOI":"10.1371\/journal.pone.0026325","article-title":"Minimal functional sites allow a classification of zinc sites in proteins","volume":"6","author":"Andreini","year":"2011","journal-title":"PLoS One"},{"key":"2023110804053531000_btad653-B2","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1016\/j.jmb.2009.02.052","article-title":"Structural analysis of metal sites in proteins: non-heme iron sites as a case study","volume":"388","author":"Andreini","year":"2009","journal-title":"J Mol Biol"},{"key":"2023110804053531000_btad653-B3","doi-asserted-by":"crossref","first-page":"1471","DOI":"10.1021\/ar900015x","article-title":"Metalloproteomes: a bioinformatic 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