Journal ArticleDOI
The confluence of big data and evolutionary genome mining for the discovery of natural products.
Marc G. Chevrette,Athina Gavrilidou,Shrikant Mantri,Nelly Selem-Mojica,Nadine Ziemert,Francisco Barona-Gómez +5 more
TLDR
This review covers literature between 2003-2021 and highlights examples where Big Data and evolutionary analyses have been combined to provide bioinformatic resources and tools for the discovery of novel natural products and their biosynthetic enzymes.About:
This article is published in Natural Product Reports.The article was published on 2021-11-17. It has received 21 citations till now.read more
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Recent advances in the chemo-biological characterization of decalin natural products and unraveling of the workings of Diels–Alderases
TL;DR: The Diels-Alder (DA) reaction refers to a [4 + 2] cycloaddition reaction that falls under the category of pericyclic reactions as discussed by the authors , which is a reaction that allows regio-and stereo-selective construction of two carbon-carbon bonds simultaneously in a concerted manner to generate a six-membered ring structure through a sixelectron cyclic transition state.
Journal ArticleDOI
Chemophenetic and Chemodiversity Approaches: New Insights on Modern Study of Plant Secondary Metabolite Diversity at Different Spatiotemporal and Organizational Scales
Ygor Jessé Ramos,João Gabriel Gouvêa-Silva,Daniel de Brito Machado,Jéssica Sales Felisberto,Renato Crespo Pereira,Nicholas J. Sadgrove,Davyson de Lima Moreira +6 more
Journal ArticleDOI
From solo to duet, intersections of natural product assembly with self-resistance.
TL;DR: Different self-resistance mechanisms showing a common feature: intersection with natural product assembly are summarized and their possible evolutionary origin and synthetic biology applications are discussed.
Journal ArticleDOI
Genomics‐Guided Efficient Identification of 2,5‐Diketopiperazine Derivatives from Actinobacteria
Jing Li,Shu-Ming Li +1 more
TL;DR: A concept of genomics-guided approach by performing genome mining and heterologous expression to uncover novel CDPS-derived DKPs and functionally characterize novel tailoring enzymes embedded in the biosynthetic pathways is described.
Journal ArticleDOI
Recent advances in the chemo-biological characterization of decalin natural products and unraveling of the workings of Diels–Alderases
TL;DR: The Diels-Alder (DA) reaction refers to a [4 + 2] cycloaddition reaction that falls under the category of pericyclic reactions as mentioned in this paper , which is a reaction that allows regio-and stereo-selective construction of two carbon-carbon bonds simultaneously in a concerted manner to generate a six-membered ring structure through a sixelectron cyclic transition state.
References
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Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
TL;DR: It is proposed that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms.
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The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes
Folker Meyer,Folker Meyer,Daniel Paarmann,Mark D'Souza,Robert Olson,Elizabeth M. Glass,Michael Kubal,Tobias Paczian,Alexis A. Rodriguez,Rick Stevens,Rick Stevens,Andreas Wilke,Jared Wilkening,Robert Edwards,Robert Edwards +14 more
TL;DR: The open-source metagenomics RAST service provides a new paradigm for the annotation and analysis of metagenomes that is stable, extensible, and freely available to all researchers.
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Bioactive microbial metabolites.
TL;DR: The short history, specific features and future prospects of research of microbial metabolites, including antibiotics and other bioactive metabolites, are summarized.
Journal ArticleDOI
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking
Mingxun Wang,Jeremy Carver,Vanessa V. Phelan,Laura M. Sanchez,Neha Garg,Yao Peng,Don D. Nguyen,Jeramie D. Watrous,Clifford A. Kapono,Tal Luzzatto-Knaan,Carla Porto,Amina Bouslimani,Alexey V. Melnik,Michael J. Meehan,Wei-Ting Liu,Max Crüsemann,Paul D. Boudreau,Eduardo Esquenazi,Mario Sandoval-Calderón,Roland D. Kersten,Laura A. Pace,Robert A. Quinn,Katherine R. Duncan,Cheng-Chih Hsu,Dimitrios J. Floros,Ronnie G. Gavilan,Karin Kleigrewe,Trent R. Northen,Rachel J. Dutton,Delphine Parrot,Erin E. Carlson,Bertrand Aigle,Charlotte Frydenlund Michelsen,Lars Jelsbak,Christian Sohlenkamp,Pavel A. Pevzner,Anna Edlund,Anna Edlund,Jeffrey S. McLean,Jeffrey S. McLean,Jörn Piel,Brian T. Murphy,Lena Gerwick,Chih-Chuang Liaw,Yu-Liang Yang,Hans-Ulrich Humpf,Maria Maansson,Robert A. Keyzers,Amy C. Sims,Andrew R. Johnson,Ashley M. Sidebottom,Brian E. Sedio,Andreas Klitgaard,Charles B. Larson,Charles B. Larson,Cristopher A. Boya P.,Daniel Torres-Mendoza,David Gonzalez,Denise Brentan Silva,Denise Brentan Silva,Lucas Miranda Marques,Daniel P. Demarque,Egle Pociute,Ellis C. O’Neill,Enora Briand,Enora Briand,Eric J. N. Helfrich,Eve A. Granatosky,Evgenia Glukhov,Florian Ryffel,Hailey Houson,Hosein Mohimani,Jenan J. Kharbush,Yi Zeng,Julia A. Vorholt,Kenji L. Kurita,Pep Charusanti,Kerry L. McPhail,Kristian Fog Nielsen,Lisa Vuong,Maryam Elfeki,Matthew F. Traxler,Niclas Engene,Nobuhiro Koyama,Oliver B. Vining,Ralph S. Baric,Ricardo Pianta Rodrigues da Silva,Samantha J. Mascuch,Sophie Tomasi,Stefan Jenkins,Venkat R. Macherla,Thomas Hoffman,Vinayak Agarwal,Philip G. Williams,Jingqui Dai,Ram P. Neupane,Joshua R. Gurr,Andrés M. C. Rodríguez,Anne Lamsa,Chen Zhang,Kathleen Dorrestein,Brendan M. Duggan,Jehad Almaliti,Pierre-Marie Allard,Prasad Phapale,Louis-Félix Nothias,Theodore Alexandrov,Marc Litaudon,Jean-Luc Wolfender,Jennifer E. Kyle,Thomas O. Metz,Tyler Peryea,Dac-Trung Nguyen,Danielle VanLeer,Paul Shinn,Ajit Jadhav,Rolf Müller,Katrina M. Waters,Wenyuan Shi,Xueting Liu,Lixin Zhang,Rob Knight,Paul R. Jensen,Bernhard O. Palsson,Kit Pogliano,Roger G. Linington,Marcelino Gutiérrez,Norberto Peporine Lopes,William H. Gerwick,William H. Gerwick,Bradley S. Moore,Bradley S. Moore,Pieter C. Dorrestein,Pieter C. Dorrestein,Nuno Bandeira,Nuno Bandeira +135 more
TL;DR: In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations and data-driven social-networking should facilitate identification of spectra and foster collaborations.
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