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MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.
Terlouw, Barbara R; Blin, Kai; Navarro-Muñoz, Jorge C; Avalon, Nicole E; Chevrette, Marc G; Egbert, Susan; Lee, Sanghoon; Meijer, David; Recchia, Michael J J; Reitz, Zachary L; van Santen, Jeffrey A; Selem-Mojica, Nelly; Tørring, Thomas; Zaroubi, Liana; Alanjary, Mohammad; Aleti, Gajender; Aguilar, César; Al-Salihi, Suhad A A; Augustijn, Hannah E; Avelar-Rivas, J Abraham; Avitia-Domínguez, Luis A; Barona-Gómez, Francisco; Bernaldo-Agüero, Jordan; Bielinski, Vincent A; Biermann, Friederike; Booth, Thomas J; Carrion Bravo, Victor J; Castelo-Branco, Raquel; Chagas, Fernanda O; Cruz-Morales, Pablo; Du, Chao; Duncan, Katherine R; Gavriilidou, Athina; Gayrard, Damien; Gutiérrez-García, Karina; Haslinger, Kristina; Helfrich, Eric J N; van der Hooft, Justin J J; Jati, Afif P; Kalkreuter, Edward; Kalyvas, Nikolaos; Kang, Kyo Bin; Kautsar, Satria; Kim, Wonyong; Kunjapur, Aditya M; Li, Yong-Xin; Lin, Geng-Min; Loureiro, Catarina; Louwen, Joris J R; Louwen, Nico L L.
Afiliación
  • 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.
  • Avalon NE; Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
  • Chevrette MG; Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0212, USA.
  • Egbert S; Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
  • Lee S; Department of Chemistry, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2, Canada.
  • Meijer D; Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
  • Recchia MJJ; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.
  • Reitz ZL; Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
  • van Santen JA; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.
  • Selem-Mojica N; Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
  • Tørring T; Unnatural Products, 2161 Delaware Ave. Suite A, Santa Cruz, CA 95060, USA.
  • Zaroubi L; Centro de Ciencias Matemáticas UNAM, Morelia, México.
  • Alanjary M; Department of Biological and Chemical Engineering, Aarhus University, Denmark.
  • Aleti G; Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada.
  • Aguilar C; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.
  • Al-Salihi SAA; Food and Animal Sciences, Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA.
  • Augustijn HE; Department of Chemistry, Purdue University, West Lafayette, IN, USA.
  • Avelar-Rivas JA; Department of Applied Sciences, University of Technology, Iraq.
  • Avitia-Domínguez LA; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.
  • Barona-Gómez F; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.
  • Bernaldo-Agüero J; 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.
  • Bielinski VA; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.
  • Biermann F; 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.
  • Booth TJ; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.
  • Carrion Bravo VJ; 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.
  • Castelo-Branco R; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
  • Chagas FO; Synthetic Biology and Bioenergy Group, J. Craig Venter Institute, La Jolla, CA 92037, USA.
  • Cruz-Morales P; Bioinformatics Group, Wageningen University, Droevendaalsesteeg, 6708 PB Wageningen, The Netherlands.
  • Du C; Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany.
  • Duncan KR; LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
  • Gavriilidou A; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
  • Gayrard D; School of Molecular Sciences, University of Western Australia, Perth, Australia.
  • Gutiérrez-García K; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.
  • Haslinger K; 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.
  • Helfrich EJN; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
  • van der Hooft JJJ; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal.
  • Jati AP; Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal.
  • Kalkreuter E; Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-599, Brazil.
  • Kalyvas N; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
  • Kang KB; Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.
  • Kautsar S; University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, 141 Cathedral Street, Glasgow, G4 ORE UK.
  • Kim W; Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany.
  • Kunjapur AM; Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
  • Li YX; Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
  • Lin GM; Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA.
  • Loureiro C; Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
  • Louwen JJR; Institute of Molecular Bio Science, Goethe-University Frankfurt, D-60438 Frankfurt am Main, Germany.
  • Louwen NLL; LOEWE Center for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
Nucleic Acids Res ; 51(D1): D603-D610, 2023 01 06.
Article en En | MEDLINE | ID: mdl-36399496
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/.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Genoma / Genómica Tipo de estudio: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Año: 2023 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Reino Unido
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Genoma / Genómica Tipo de estudio: Prognostic_studies Idioma: En Revista: Nucleic Acids Res Año: 2023 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Reino Unido