{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T00:24:31Z","timestamp":1783038271303,"version":"3.54.6"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,9,27]],"date-time":"2021-09-27T00:00:00Z","timestamp":1632700800000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["POIR.04.04.00-00-5CF1\/18-00"],"award-info":[{"award-number":["POIR.04.04.00-00-5CF1\/18-00"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004281","name":"Polish National Science Centre","doi-asserted-by":"crossref","award":["2017\/27\/N\/NZ1\/00716"],"award-info":[{"award-number":["2017\/27\/N\/NZ1\/00716"]}],"id":[{"id":"10.13039\/501100004281","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The Rossmann fold enzymes are involved in essential biochemical pathways such as nucleotide and amino acid metabolism. Their functioning relies on interaction with cofactors, small nucleoside-based compounds specifically recognized by a conserved \u03b2\u03b1\u03b2 motif shared by all Rossmann fold proteins. While Rossmann methyltransferases recognize only a single cofactor type, the S-adenosylmethionine, the oxidoreductases, depending on the family, bind nicotinamide (nicotinamide adenine dinucleotide, nicotinamide adenine dinucleotide phosphate) or flavin-based (flavin adenine dinucleotide) cofactors. In this study, we showed that despite its short length, the \u03b2\u03b1\u03b2 motif unambiguously defines the specificity towards the cofactor. Following this observation, we trained two complementary deep learning models for the prediction of the cofactor specificity based on the sequence and structural features of the \u03b2\u03b1\u03b2 motif. A benchmark on two independent test sets, one containing \u03b2\u03b1\u03b2 motifs bearing no resemblance to those of the training set, and the other comprising 38 experimentally confirmed cases of rational design of the cofactor specificity, revealed the nearly perfect performance of the two methods. The Rossmann-toolbox protocols can be accessed via the webserver at https:\/\/lbs.cent.uw.edu.pl\/rossmann-toolbox and are available as a Python package at https:\/\/github.com\/labstructbioinf\/rossmann-toolbox.<\/jats:p>","DOI":"10.1093\/bib\/bbab371","type":"journal-article","created":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T07:20:51Z","timestamp":1631085651000},"source":"Crossref","is-referenced-by-count":54,"title":["Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins"],"prefix":"10.1093","volume":"23","author":[{"given":"Kamil","family":"Kami\u0144ski","sequence":"first","affiliation":[{"name":"Laboratory of Structural Bioinformatics, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, 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