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  4. Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power
 
research article

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power

Hafner, Jasmin  
•
MohammadiPeyhani, Homa
•
Sveshnikova, Anastasia  
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June 19, 2020
Acs Synthetic Biology

The ATLAS of Biochemistry is a repository of both known and novel predicted biochemical reactions between biological compounds listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG). ATLAS was originally compiled based on KEGG 2015, though the number of KEGG reactions has increased by almost 20 percent since then. Here, we present an updated version of ATLAS created from KEGG 2018 using an increased set of generalized reaction rules. Furthermore, we improved the accuracy of the enzymes that are predicted for catalyzing novel reactions. ATLAS now contains similar to 150 000 reactions, out of which 96% are novel. In this report, we present detailed statistics on the updated ATLAS and highlight the improvements with regard to the previous version. Most importantly, 107 reactions predicted in the original ATLAS are now known to KEGG, which validates the predictive power of our approach. The updated ATLAS is available at https://lcsb-database.epfl.ch.atlas.

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Type
research article
DOI
10.1021/acssynbio.0c00052
Web of Science ID

WOS:000543677300027

Author(s)
Hafner, Jasmin  
MohammadiPeyhani, Homa
Sveshnikova, Anastasia  
Scheidegger, Alan
Hatzimanikatis, Vassily  
Date Issued

2020-06-19

Publisher

AMER CHEMICAL SOC

Published in
Acs Synthetic Biology
Volume

9

Issue

6

Start page

1479

End page

1482

Subjects

Biochemical Research Methods

•

Biochemistry & Molecular Biology

•

reaction prediction

•

enzyme prediction

•

enzyme promiscuity

•

metabolic networks

•

biochemical database

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCSB  
Available on Infoscience
July 12, 2020
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/169996
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