MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics

Journal of Cheminformatics
James G JeffryesChristopher S Henry

Abstract

In spite of its great promise, metabolomics has proven difficult to execute in an untargeted and generalizable manner. Liquid chromatography-mass spectrometry (LC-MS) has made it possible to gather data on thousands of cellular metabolites. However, matching metabolites to their spectral features continues to be a bottleneck, meaning that much of the collected information remains uninterpreted and that new metabolites are seldom discovered in untargeted studies. These challenges require new approaches that consider compounds beyond those available in curated biochemistry databases. Here we present Metabolic In silico Network Expansions (MINEs), an extension of known metabolite databases to include molecules that have not been observed, but are likely to occur based on known metabolites and common biochemical reactions. We utilize an algorithm called the Biochemical Network Integrated Computational Explorer (BNICE) and expert-curated reaction rules based on the Enzyme Commission classification system to propose the novel chemical structures and reactions that comprise MINE databases. Starting from the Kyoto Encyclopedia of Genes and Genomes (KEGG) COMPOUND database, the MINE contains over 571,000 compounds, of which 93% are not ...Continue Reading

References

Apr 1, 1999·Chemistry & Biology·P J O'Brien, D Herschlag
Jul 7, 2005·Journal of the American Chemical Society·Joanna González-LergierVassily Hatzimanikatis
Nov 22, 2005·Biophysical Journal·Christopher S HenryVassily Hatzimanikatis
Jul 27, 2006·Proceedings of the National Academy of Sciences of the United States of America·Evelyne DerelleHervé Moreau
Mar 21, 2007·Journal of Chemical Information and Modeling·Stephen E SteinPeter J Linstrom
Mar 11, 2008·Chemistry Central Journal·Noel M O'BoyleGeoffrey R Hutchison
Dec 6, 2008·Chembiochem : a European Journal of Chemical Biology·Israel Sánchez-MorenoEduardo García-Junceda
Aug 22, 2009·Bioinformatics·M J L de GrootD de Ridder
Nov 26, 2009·Nucleic Acids Research·Yanli WangStephen H Bryant
Jan 5, 2010·Metabolomics : Official Journal of the Metabolomic Society·Augustin ScalbertSuzan Wopereis
Jan 22, 2010·Biotechnology and Bioengineering·Christopher S HenryVassily Hatzimanikatis
Mar 24, 2010·BMC Bioinformatics·Sebastian WolfSteffen Neumann
May 4, 2010·Nucleic Acids Research·Yuki MoriyaMinoru Kanehisa
Jul 14, 2010·Journal of Mass Spectrometry : JMS·Hisayuki HoraiTakaaki Nishioka
Apr 14, 2011·Nucleic Acids Research·Junfeng GaoLawrence P Wackett
May 14, 2011·The Journal of Biological Chemistry·Oliver FiehnTobias Kind
Aug 10, 2011·BMC Biochemistry·Maren LangDietmar Schomburg
Nov 9, 2011·Nucleic Acids Research·Timothy JewisonDavid S Wishart
Mar 23, 2012·Nature Reviews. Molecular Cell Biology·Gary J PattiGary Siuzdak
May 23, 2012·BMC Bioinformatics·Kalai Vanii JayaseelanChristoph Steinbeck
Jun 30, 2012·Science·Jing-Ke WengJoseph P Noel
Sep 1, 2012·Science·Hojung NamBernhard O Palsson
Oct 9, 2012·Analytical Chemistry·Lochana C MenikarachchiDavid F Grant
Nov 13, 2012·Nucleic Acids Research·Ingrid M KeselerPeter D Karp
Jan 25, 2013·Journal of Cheminformatics·Stephen HellerIgor Pletnev
Mar 28, 2013·BMC Bioinformatics·Tomer AltmanPeter D Karp
Sep 3, 2013·Journal of Chemical Information and Modeling·Lochana C MenikarachchiDavid F Grant
Nov 12, 2013·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Jan 1, 2012·Metabolites·Robert A Dromms, Mark P Styczynski
Jan 1, 2013·Metabolites·Emma L Schymanski, Steffen Neumann
Aug 27, 2014·Analytical Chemistry·Yingfeng WangChongle Pan
Nov 29, 2014·The Biochemical Journal·Océane FrelinAndrew D Hanson

❮ Previous
Next ❯

Citations

Dec 15, 2015·Metabolic Engineering·Matthew MouraKeith E J Tyo
Feb 18, 2016·Analytical Chemistry·Pierre-Marie AllardJean-Luc Wolfender
Dec 17, 2015·Annual Review of Plant Biology·Andrew D HansonValérie de Crécy-Lagard
Apr 30, 2016·International Journal of Molecular Sciences·Ina Aretz, David Meierhofer
Jul 2, 2016·Expert Opinion on Drug Discovery·M Cuperlovic-Culf, A S Culf
Apr 25, 2017·Mass Spectrometry Reviews·Tobias KindOliver Fiehn
Dec 3, 2016·Mass Spectrometry·Fumio Matsuda
Nov 16, 2017·Nucleic Acids Research·David S WishartAugustin Scalbert
Dec 1, 2017·Briefings in Bioinformatics·Aitor Blanco-MíguezAnália Lourenço
Dec 21, 2017·Journal of Cheminformatics·Mathilde KochJean-Loup Faulon
Feb 16, 2018·Bioinformatics·Ivan LaponogovKirill A Veselkov
Jun 27, 2018·Plant Signaling & Behavior·M HüdigV G Maurino
Nov 1, 2017·Journal of Cheminformatics·Sarah M KimLydia E Kavraki
Mar 31, 2019·Biotechnology Journal·Kristin V Presnell, Hal S Alper
Oct 4, 2016·Metabolomics : Official Journal of the Metabolomic Society·Douglas B Kell, Stephen G Oliver
Jun 28, 2019·Briefings in Bioinformatics·Fu ChenQian-Nan Hu
Apr 18, 2020·The Biochemical Journal·Jenelle A PattersonAndrew D Hanson
Oct 2, 2020·Database : the Journal of Biological Databases and Curation·Dandan SunQian-Nan Hu
Aug 7, 2019·Microbial Biotechnology·Jian-Ming LiuPeter Ruhdal Jensen
Jan 19, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Ivan LiakhAdriana Mika
Jun 18, 2017·Electrophoresis·Biswapriya B MisraDmitry Grapov
Nov 1, 2017·Journal of Cheminformatics·Emma L SchymanskiSteffen Neumann
Mar 8, 2020·Journal of Separation Science·Michael Witting, Sebastian Böcker
Jun 11, 2016·Biochemical Society Transactions·Claudia Lerma-OrtizAndrew D Hanson
Jul 18, 2018·Marine Drugs·Florbela Pereira, Joao Aires-de-Sousa
Mar 5, 2019·Metabolomics : Official Journal of the Metabolomic Society·Oliver A H Jones
Jan 2, 2021·Computational and Structural Biotechnology Journal·Sandrien DesmetKris Morreel

❮ Previous
Next ❯

Software Mentioned

Metabolizer
InChIKey
MINEs
IIMDB
MyCompoundID
EcoCyc
BNICE
Perl
Java ARchive ( JAR )
Biochemical Network Integrated Network Explorer ( BNICE )

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.