Literature DB >> 33423696

COCONUT online: Collection of Open Natural Products database.

Maria Sorokina1, Peter Merseburger2, Kohulan Rajan2, Mehmet Aziz Yirik2, Christoph Steinbeck2.   

Abstract

Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world and in different application fields, therefore, over the years a multiplication of generalistic and thematic NP databases has been observed. However, there is, at this moment, no online resource regrouping all known NPs in just one place, which would greatly simplify NPs research and allow computational screening and other in silico applications. In this manuscript we present the online version of the COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download NPs. COCONUT web is freely available at https://coconut.naturalproducts.net .

Entities:  

Keywords:  Database; Molecular similarity search; Molecular substructure search; MongoDB; Natural products; NoSQL

Year:  2021        PMID: 33423696      PMCID: PMC7798278          DOI: 10.1186/s13321-020-00478-9

Source DB:  PubMed          Journal:  J Cheminform        ISSN: 1758-2946            Impact factor:   5.514


  30 in total

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Journal:  Plant Cell Physiol       Date:  2013-01-03       Impact factor: 4.927

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Journal:  PLoS One       Date:  2011-01-06       Impact factor: 3.240

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Journal:  J Cheminform       Date:  2016-11-04       Impact factor: 5.514

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Journal:  Sci Rep       Date:  2017-08-03       Impact factor: 4.379

6.  The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

Authors:  Egon L Willighagen; John W Mayfield; Jonathan Alvarsson; Arvid Berg; Lars Carlsson; Nina Jeliazkova; Stefan Kuhn; Tomáš Pluskal; Miquel Rojas-Chertó; Ola Spjuth; Gilleain Torrance; Chris T Evelo; Rajarshi Guha; Christoph Steinbeck
Journal:  J Cheminform       Date:  2017-06-06       Impact factor: 5.514

7.  An open source chemical structure curation pipeline using RDKit.

Authors:  A Patrícia Bento; Anne Hersey; Eloy Félix; Greg Landrum; Anna Gaulton; Francis Atkinson; Louisa J Bellis; Marleen De Veij; Andrew R Leach
Journal:  J Cheminform       Date:  2020-09-01       Impact factor: 5.514

8.  The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery.

Authors:  Jeffrey A van Santen; Grégoire Jacob; Amrit Leen Singh; Victor Aniebok; Marcy J Balunas; Derek Bunsko; Fausto Carnevale Neto; Laia Castaño-Espriu; Chen Chang; Trevor N Clark; Jessica L Cleary Little; David A Delgadillo; Pieter C Dorrestein; Katherine R Duncan; Joseph M Egan; Melissa M Galey; F P Jake Haeckl; Alex Hua; Alison H Hughes; Dasha Iskakova; Aswad Khadilkar; Jung-Ho Lee; Sanghoon Lee; Nicole LeGrow; Dennis Y Liu; Jocelyn M Macho; Catherine S McCaughey; Marnix H Medema; Ram P Neupane; Timothy J O'Donnell; Jasmine S Paula; Laura M Sanchez; Anam F Shaikh; Sylvia Soldatou; Barbara R Terlouw; Tuan Anh Tran; Mercia Valentine; Justin J J van der Hooft; Duy A Vo; Mingxun Wang; Darryl Wilson; Katherine E Zink; Roger G Linington
Journal:  ACS Cent Sci       Date:  2019-11-14       Impact factor: 14.553

Review 9.  Review on natural products databases: where to find data in 2020.

Authors:  Maria Sorokina; Christoph Steinbeck
Journal:  J Cheminform       Date:  2020-04-03       Impact factor: 5.514

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Journal:  Nucleic Acids Res       Date:  2014-10-09       Impact factor: 16.971

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  29 in total

Review 1.  Advancements in capturing and mining mass spectrometry data are transforming natural products research.

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Journal:  Nat Prod Rep       Date:  2021-11-17       Impact factor: 13.423

2.  PIKAChU: a Python-based informatics kit for analysing chemical units.

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3.  CFM-ID 4.0 - a web server for accurate MS-based metabolite identification.

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Journal:  Nucleic Acids Res       Date:  2022-05-24       Impact factor: 19.160

4.  The LOTUS initiative for open knowledge management in natural products research.

Authors:  Adriano Rutz; Maria Sorokina; Jakub Galgonek; Daniel Mietchen; Egon Willighagen; Arnaud Gaudry; James G Graham; Ralf Stephan; Roderic Page; Jiří Vondrášek; Christoph Steinbeck; Guido F Pauli; Jean-Luc Wolfender; Jonathan Bisson; Pierre-Marie Allard
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5.  NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products.

Authors:  Hyun Woo Kim; Mingxun Wang; Christopher A Leber; Louis-Félix Nothias; Raphael Reher; Kyo Bin Kang; Justin J J van der Hooft; Pieter C Dorrestein; William H Gerwick; Garrison W Cottrell
Journal:  J Nat Prod       Date:  2021-10-18       Impact factor: 4.803

6.  MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis.

Authors:  Jan Přívratský; Jiří Novák
Journal:  J Cheminform       Date:  2021-07-07       Impact factor: 5.514

7.  Target Prediction Model for Natural Products Using Transfer Learning.

Authors:  Bo Qiang; Junyong Lai; Hongwei Jin; Liangren Zhang; Zhenming Liu
Journal:  Int J Mol Sci       Date:  2021-04-28       Impact factor: 5.923

8.  Selection for seed size has uneven effects on specialized metabolite abundance in oat (Avena sativa L.).

Authors:  Lauren J Brzozowski; Haixiao Hu; Malachy T Campbell; Corey D Broeckling; Melanie Caffe; Lucía Gutiérrez; Kevin P Smith; Mark E Sorrells; Michael A Gore; Jean-Luc Jannink
Journal:  G3 (Bethesda)       Date:  2022-03-04       Impact factor: 3.542

Review 9.  The Combination of Tradition and Future: Data-Driven Natural-Product-Based Treatments for Parkinson's Disease.

Authors:  Zhijun Miao; Jinwei Bai; Li Shen; Rajeev K Singla
Journal:  Evid Based Complement Alternat Med       Date:  2021-07-14       Impact factor: 2.629

10.  Progress on open chemoinformatic tools for expanding and exploring the chemical space.

Authors:  José L Medina-Franco; Norberto Sánchez-Cruz; Edgar López-López; Bárbara I Díaz-Eufracio
Journal:  J Comput Aided Mol Des       Date:  2021-06-18       Impact factor: 4.179

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