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Literature DB >> 33152079

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes.

Kai Blin¹, Simon Shaw¹, Satria A Kautsar², Marnix H Medema², Tilmann Weber¹.

Abstract

Microorganisms produce natural products that are frequently used in the development of antibacterial, antiviral, and anticancer drugs, pesticides, herbicides, or fungicides. In recent years, genome mining has evolved into a prominent method to access this potential. antiSMASH is one of the most popular tools for this task. Here, we present version 3 of the antiSMASH database, providing a means to access and query precomputed antiSMASH-5.2-detected biosynthetic gene clusters from representative, publicly available, high-quality microbial genomes via an interactive graphical user interface. In version 3, the database contains 147 517 high quality BGC regions from 388 archaeal, 25 236 bacterial and 177 fungal genomes and is available at https://antismash-db.secondarymetabolites.org/.

Entities: Chemical Disease Species

Year: 2021 PMID： 33152079 PMCID： PMC7779067 DOI： 10.1093/nar/gkaa978

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

20 in total

Review 1. In silico tools for the analysis of antibiotic biosynthetic pathways.

Authors: Tilmann Weber
Journal: Int J Med Microbiol Date: 2014-02-19 Impact factor: 3.473

2. Natural Products as Sources of New Drugs over the Nearly Four Decades from 01/1981 to 09/2019.

Authors: David J Newman; Gordon M Cragg
Journal: J Nat Prod Date: 2020-03-12 Impact factor: 4.050

3. Computational approaches to natural product discovery.

Authors: Marnix H Medema; Michael A Fischbach
Journal: Nat Chem Biol Date: 2015-09 Impact factor: 15.040

4. IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase.

Authors: Krishnaveni Palaniappan; I-Min A Chen; Ken Chu; Anna Ratner; Rekha Seshadri; Nikos C Kyrpides; Natalia N Ivanova; Nigel J Mouncey
Journal: Nucleic Acids Res Date: 2020-01-08 Impact factor: 16.971

5. Mash: fast genome and metagenome distance estimation using MinHash.

Authors: Brian D Ondov; Todd J Treangen; Páll Melsted; Adam B Mallonee; Nicholas H Bergman; Sergey Koren; Adam M Phillippy
Journal: Genome Biol Date: 2016-06-20 Impact factor: 13.583

6. antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.

Authors: Kai Blin; Thomas Wolf; Marc G Chevrette; Xiaowen Lu; Christopher J Schwalen; Satria A Kautsar; Hernando G Suarez Duran; Emmanuel L C de Los Santos; Hyun Uk Kim; Mariana Nave; Jeroen S Dickschat; Douglas A Mitchell; Ekaterina Shelest; Rainer Breitling; Eriko Takano; Sang Yup Lee; Tilmann Weber; Marnix H Medema
Journal: Nucleic Acids Res Date: 2017-07-03 Impact factor: 16.971

Review 7. The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production.

Authors: Tilmann Weber; Hyun Uk Kim
Journal: Synth Syst Biotechnol Date: 2016-02-05

8. The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters.

Authors: Kai Blin; Victòria Pascal Andreu; Emmanuel L C de Los Santos; Francesco Del Carratore; Sang Yup Lee; Marnix H Medema; Tilmann Weber
Journal: Nucleic Acids Res Date: 2019-01-08 Impact factor: 16.971

9. antiSMASH 2.0--a versatile platform for genome mining of secondary metabolite producers.

Authors: Kai Blin; Marnix H Medema; Daniyal Kazempour; Michael A Fischbach; Rainer Breitling; Eriko Takano; Tilmann Weber
Journal: Nucleic Acids Res Date: 2013-06-03 Impact factor: 16.971

10. Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters.

Authors: Kai Blin; Hyun Uk Kim; Marnix H Medema; Tilmann Weber
Journal: Brief Bioinform Date: 2019-07-19 Impact factor: 11.622

24 in total

Review 1. Strategies to access biosynthetic novelty in bacterial genomes for drug discovery.

Authors: Franziska Hemmerling; Jörn Piel
Journal: Nat Rev Drug Discov Date: 2022-03-16 Impact factor: 84.694

2. ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria.

Authors: Morgan Anne Feeney; Jake Terry Newitt; Emily Addington; Lis Algora-Gallardo; Craig Allan; Lucas Balis; Anna S Birke; Laia Castaño-Espriu; Louise K Charkoudian; Rebecca Devine; Damien Gayrard; Jacob Hamilton; Oliver Hennrich; Paul A Hoskisson; Molly Keith-Baker; Joshua G Klein; Worarat Kruasuwan; David R Mark; Yvonne Mast; Rebecca E McHugh; Thomas C McLean; Elmira Mohit; John T Munnoch; Jordan Murray; Katie Noble; Hiroshi Otani; Jonathan Parra; Camila F Pereira; Louisa Perry; Linamaria Pintor-Escobar; Leighton Pritchard; Samuel M M Prudence; Alicia H Russell; Jana K Schniete; Ryan F Seipke; Nelly Sélem-Mojica; Agustina Undabarrena; Kristiina Vind; Gilles P van Wezel; Barrie Wilkinson; Sarah F Worsley; Katherine R Duncan; Lorena T Fernández-Martínez; Matthew I Hutchings
Journal: Microb Genom Date: 2022-07

3. Evolutionary Genome Mining for the Discovery and Engineering of Natural Product Biosynthesis.

Authors: Marc G Chevrette; Nelly Selem-Mojica; César Aguilar; Kristin Labby; Edder D Bustos-Diaz; Jo Handelsman; Francisco Barona-Gómez
Journal: Methods Mol Biol Date: 2022

4. Sesbanimide R, a Novel Cytotoxic Polyketide Produced by Magnetotactic Bacteria.

Authors: Ram Prasad Awal; Patrick A Haack; Chantal D Bader; Cornelius N Riese; Dirk Schüler; Rolf Müller
Journal: mBio Date: 2021-05-18 Impact factor: 7.867

5. antiSMASH 6.0: improving cluster detection and comparison capabilities.

Authors: Kai Blin; Simon Shaw; Alexander M Kloosterman; Zach Charlop-Powers; Gilles P van Wezel; Marnix H Medema; Tilmann Weber
Journal: Nucleic Acids Res Date: 2021-07-02 Impact factor: 16.971

6. Differential response to prey quorum signals indicates predatory specialization of myxobacteria and ability to predate Pseudomonas aeruginosa.

Authors: Shukria Akbar; Kayleigh E Phillips; Sandeep K Misra; Joshua S Sharp; D Cole Stevens
Journal: Environ Microbiol Date: 2021-10-21 Impact factor: 5.476

7. Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite.

Authors: Agustina Undabarrena; Ricardo Valencia; Andrés Cumsille; Leonardo Zamora-Leiva; Eduardo Castro-Nallar; Francisco Barona-Gomez; Beatriz Cámara
Journal: Microb Genom Date: 2021-07