MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.

Autor:	Terlouw BR; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., Blin K; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark., Navarro-Muñoz JC; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands., Avalon NE; Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0212, USA., Chevrette MG; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA., Egbert S; Department of Chemistry, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada., Lee S; Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada., Meijer D; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., Recchia MJJ; Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada., Reitz ZL; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., van Santen JA; Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.; Unnatural Products, 2161 Delaware Ave. Suite A, Santa Cruz, CA 95060, USA., Selem-Mojica N; Centro de Ciencias Matemáticas UNAM, Morelia, México., Tørring T; Department of Biological and Chemical Engineering, Aarhus University, Denmark., Zaroubi L; Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada., Alanjary M; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., Aleti G; Food and Animal Sciences, Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA., Aguilar C; Department of Chemistry, Purdue University, West Lafayette, IN, USA., Al-Salihi SAA; Department of Applied Sciences, University of Technology, Iraq., Augustijn HE; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands., Avelar-Rivas JA; Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México., Avitia-Domínguez LA; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.; Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México., Barona-Gómez F; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.; Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México., Bernaldo-Agüero J; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México., Bielinski VA; Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, CA 92037, USA., Biermann F; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.; Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany.; LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany., Booth TJ; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.; School of Molecular Sciences, University of Western Australia, Perth, Australia., Carrion Bravo VJ; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.; Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain.; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands., Castelo-Branco R; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal.; Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal., Chagas FO; Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil., Cruz-Morales P; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark., Du C; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands., Duncan KR; University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK., Gavriilidou A; Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany.; Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany., Gayrard D; Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK., Gutiérrez-García K; Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA., Haslinger K; Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands., Helfrich EJN; Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany.; LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany., van der Hooft JJJ; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.; Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa., Jati AP; Indonesian Society of Bioinformatics And Biodiversity, Indonesia., Kalkreuter E; Department of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA., Kalyvas N; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands., Kang KB; College of Pharmacy, Sookmyung Women's University, Seoul, South Korea., Kautsar S; Department of Chemistry, University of Florida Scripps Biomedical Research, 110 Scripps Way, Jupiter, FL 33458, USA., Kim W; Korean Lichen Research Institute, Sunchon National Universtiy, Suncheon, South Korea., Kunjapur AM; Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA., Li YX; Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P.R. China., Lin GM; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA., Loureiro C; Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands., Louwen JJR; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., Louwen NLL; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., Lund G; Sustainable Soils and Crops, Rothamsted Research, Harpenden, Hertfordshire, UK., Parra J; Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica, San José, 11501-2060, Costa Rica.; Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, 11501-2060, Costa Rica.; Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica., Philmus B; Department of Pharmaceutical Sciences, Oregon State University, USA., Pourmohsenin B; Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany.; Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany., Pronk LJU; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., Rego A; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal.; Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Portugal., Rex DAB; Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore 575018, India., Robinson S; Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland., Rosas-Becerra LR; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.; Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato, Gto., México., Roxborough ET; School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK., Schorn MA; Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands., Scobie DJ; University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK., Singh KS; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., Sokolova N; Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands., Tang X; Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China., Udwary D; DOE Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, CA, USA., Vigneshwari A; Department of Microbiology, University of Szeged, Hungary., Vind K; Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands.; NAICONS Srl, 20139 Milan, Italy., Vromans SPJM; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., Waschulin V; School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK., Williams SE; School of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, UK., Winter JM; Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA., Witte TE; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada., Xie H; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.; Key laboratory of Detection for Biotoxins, Ministry of Agriculture and Rural Affairs and Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China., Yang D; Department of Chemistry and Natural Products Discovery Center, UF Scripps Biomedical Research, University of Florida, Jupiter, FL 33458, USA., Yu J; SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China., Zdouc M; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands., Zhong Z; Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands., Collemare J; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands., Linington RG; Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada., Weber T; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark., Medema MH; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.
Jazyk:	angličtina
Zdroj:	Nucleic acids research [Nucleic Acids Res] 2023 Jan 06; Vol. 51 (D1), pp. D603-D610.
DOI:	10.1093/nar/gkac1049
Abstrakt:	With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/. (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)
Databáze:	MEDLINE
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