{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T07:55:54Z","timestamp":1774770954630,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,5,11]],"date-time":"2020-05-11T00:00:00Z","timestamp":1589155200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004567","name":"Ministry of Education","doi-asserted-by":"publisher","award":["857560"],"award-info":[{"award-number":["857560"]}],"id":[{"id":"10.13039\/501100004567","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004567","name":"Ministry of Education","doi-asserted-by":"publisher","award":["02.1.01\/0.0\/0.0\/18_046\/0015975"],"award-info":[{"award-number":["02.1.01\/0.0\/0.0\/18_046\/0015975"]}],"id":[{"id":"10.13039\/501100004567","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004567","name":"Ministry of Education","doi-asserted-by":"publisher","award":["CZ.02.1.01\/0.0\/0.0\/16_026\/0008451"],"award-info":[{"award-number":["CZ.02.1.01\/0.0\/0.0\/16_026\/0008451"]}],"id":[{"id":"10.13039\/501100004567","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004567","name":"Ministry of Education","doi-asserted-by":"publisher","award":["CZ.02.1.01\/0.0\/0.0\/16_019\/0000868"],"award-info":[{"award-number":["CZ.02.1.01\/0.0\/0.0\/16_019\/0000868"]}],"id":[{"id":"10.13039\/501100004567","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004567","name":"Ministry of Education","doi-asserted-by":"publisher","award":["LQ1602"],"award-info":[{"award-number":["LQ1602"]}],"id":[{"id":"10.13039\/501100004567","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["720776"],"award-info":[{"award-number":["720776"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["814418"],"award-info":[{"award-number":["814418"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004585","name":"Brno University of Technology","doi-asserted-by":"publisher","award":["FIT-S-20-6293"],"award-info":[{"award-number":["FIT-S-20-6293"]}],"id":[{"id":"10.13039\/501100004585","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004585","name":"Brno University of Technology","doi-asserted-by":"publisher","award":["LM2018140"],"award-info":[{"award-number":["LM2018140"]}],"id":[{"id":"10.13039\/501100004585","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004585","name":"Brno University of Technology","doi-asserted-by":"publisher","award":["LM2015047"],"award-info":[{"award-number":["LM2015047"]}],"id":[{"id":"10.13039\/501100004585","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Millions of protein sequences are being discovered at an incredible pace, representing an inexhaustible source of biocatalysts. Despite genomic databases growing exponentially, classical biochemical characterization techniques are time-demanding, cost-ineffective and low-throughput. Therefore, computational methods are being developed to explore the unmapped sequence space efficiently. Selection of putative enzymes for biochemical characterization based on rational and robust analysis of all available sequences remains an unsolved problem. To address this challenge, we have developed EnzymeMiner\u2014a web server for automated screening and annotation of diverse family members that enables selection of hits for wet-lab experiments. EnzymeMiner prioritizes sequences that are more likely to preserve the catalytic activity and are heterologously expressible in a soluble form in Escherichia coli. The solubility prediction employs the in-house SoluProt predictor developed using machine learning. EnzymeMiner reduces the time devoted to data gathering, multi-step analysis, sequence prioritization and selection from days to hours. The successful use case for the haloalkane dehalogenase family is described in a comprehensive tutorial available on the EnzymeMiner web page. EnzymeMiner is a universal tool applicable to any enzyme family that provides an interactive and easy-to-use web interface freely available at https:\/\/loschmidt.chemi.muni.cz\/enzymeminer\/.<\/jats:p>","DOI":"10.1093\/nar\/gkaa372","type":"journal-article","created":{"date-parts":[[2020,4,29]],"date-time":"2020-04-29T11:23:47Z","timestamp":1588159427000},"page":"W104-W109","source":"Crossref","is-referenced-by-count":101,"title":["EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities"],"prefix":"10.1093","volume":"48","author":[{"given":"Jiri","family":"Hon","sequence":"first","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and Research Center for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"},{"name":"IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, Bozetechova 2, Brno, Czech Republic"},{"name":"International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic"}]},{"given":"Simeon","family":"Borko","sequence":"first","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and Research Center for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"},{"name":"IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, Bozetechova 2, Brno, Czech Republic"}]},{"given":"Jan","family":"Stourac","sequence":"first","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and Research Center for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"},{"name":"International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic"}]},{"given":"Zbynek","family":"Prokop","sequence":"first","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and Research Center for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"},{"name":"International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic"}]},{"given":"Jaroslav","family":"Zendulka","sequence":"first","affiliation":[{"name":"IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, Bozetechova 2, Brno, Czech Republic"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6803-0340","authenticated-orcid":false,"given":"David","family":"Bednar","sequence":"first","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and Research Center for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"},{"name":"International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic"}]},{"given":"Tomas","family":"Martinek","sequence":"first","affiliation":[{"name":"IT4Innovations Centre of Excellence, Faculty of Information Technology, Brno University of Technology, Bozetechova 2, Brno, Czech Republic"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7848-8216","authenticated-orcid":false,"given":"Jiri","family":"Damborsky","sequence":"first","affiliation":[{"name":"Loschmidt Laboratories, Department of Experimental Biology and Research Center for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic"},{"name":"International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic"}]}],"member":"286","published-online":{"date-parts":[[2020,5,11]]},"reference":[{"key":"2020062614043775400_B1","doi-asserted-by":"crossref","first-page":"D23","DOI":"10.1093\/nar\/gky1069","article-title":"Database resources of the national center for biotechnology information","volume":"47","author":"Sayers","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614043775400_B2","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"UniProt Consortium","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614043775400_B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms10008","article-title":"Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics","volume":"6","author":"Colin","year":"2015","journal-title":"Nat. Commun."},{"key":"2020062614043775400_B4","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/s12934-017-0629-5","article-title":"Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica","volume":"16","author":"Beneyton","year":"2017","journal-title":"Microb. Cell Fact."},{"key":"2020062614043775400_B5","doi-asserted-by":"crossref","first-page":"2402","DOI":"10.1021\/acscatal.7b03523","article-title":"Exploration of enzyme diversity by integrating bioinformatics with expression analysis and biochemical characterization","volume":"8","author":"Vanacek","year":"2018","journal-title":"ACS Catal."},{"key":"2020062614043775400_B6","doi-asserted-by":"crossref","first-page":"D427","DOI":"10.1093\/nar\/gky995","article-title":"The Pfam protein families database in 2019","volume":"47","author":"El-Gebali","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020062614043775400_B7","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1093\/bioinformatics\/btx680","article-title":"DEEPre: sequence-based enzyme EC number prediction by deep learning","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2020062614043775400_B8","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1186\/s13059-019-1835-8","article-title":"The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens","volume":"20","author":"Zhou","year":"2019","journal-title":"Genome Biol."},{"key":"2020062614043775400_B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms10005","article-title":"Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway","volume":"6","author":"Mak","year":"2015","journal-title":"Nat. Commun."},{"key":"2020062614043775400_B10","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2020062614043775400_B11","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"Edgar","year":"2010","journal-title":"Bioinformatics"},{"key":"2020062614043775400_B12","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"Sievers","year":"2011","journal-title":"Mol. Syst. Biol."},{"key":"2020062614043775400_B13","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"Krogh","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2020062614043775400_B14","doi-asserted-by":"crossref","first-page":"W116","DOI":"10.1093\/nar\/gki442","article-title":"InterProScan: protein domains identifier","volume":"33","author":"Quevillon","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2020062614043775400_B15","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","article-title":"The NCBI Taxonomy database","volume":"40","author":"Federhen","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2020062614043775400_B16","doi-asserted-by":"crossref","first-page":"D57","DOI":"10.1093\/nar\/gkr1163","article-title":"BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata","volume":"40","author":"Barrett","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2020062614043775400_B17","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1021\/acscatal.8b03613","article-title":"Computational design of Stable and Soluble Biocatalysts","volume":"9","author":"Musil","year":"2019","journal-title":"ACS Catal."},{"key":"2020062614043775400_B18","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"2020062614043775400_B19","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2020062614043775400_B20","doi-asserted-by":"crossref","first-page":"4651","DOI":"10.1021\/acs.biochem.8b00473","article-title":"Revealing unexplored sequence-function space using sequence similarity networks","volume":"57","author":"Copp","year":"2018","journal-title":"Biochemistry"},{"key":"2020062614043775400_B21","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1016\/j.bbapap.2015.04.015","article-title":"Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks","volume":"1854","author":"Gerlt","year":"2015","journal-title":"Biochim. Biophys. Acta (BBA) - Proteins Proteomics"},{"key":"2020062614043775400_B22","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":"2020062614043775400_B23","doi-asserted-by":"crossref","first-page":"2265","DOI":"10.1073\/pnas.1614437114","article-title":"Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning","volume":"114","author":"Klesmith","year":"2017","journal-title":"Proc. Natl Acad. Sci. U.S.A."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W104\/33433447\/gkaa372.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W104\/33433447\/gkaa372.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,27]],"date-time":"2020-06-27T06:39:09Z","timestamp":1593239949000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/W1\/W104\/5835821"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,11]]},"references-count":23,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2020,5,11]]},"published-print":{"date-parts":[[2020,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaa372","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7,2]]},"published":{"date-parts":[[2020,5,11]]}}}