ArticleACS synthetic biology2020
Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power.
Article in ACS synthetic biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- WASP: a pipeline for functional annotation prediction based on AlphaFold structural models.Nature communications · 2026Article
- CBR-db: A Cheminformatic Database for Biochemical Reaction Analysis.ACS synthetic biology · 2026Article
- Computational approaches to enzymatic reaction assignment: a review of methods, validations, and future directions.Briefings in bioinformatics · 2025Review
- Enzyme promiscuity in the field of synthetic biology applied to white biotechnology: Opportunities and weaknesses.Biodesign research · 2025Review
- Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking.Nature communications · 2025Article
- Deep learning in template-free de novo biosynthetic pathway design of natural products.Briefings in bioinformatics · 2024Review
- Review
- Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota.NPJ systems biology and applications · 2024Article
- Primitive purine biosynthesis connects ancient geochemistry to modern metabolism.Nature ecology & evolution · 2024Article
- Machine Learning-Guided Protein Engineering.ACS catalysis · 2023Review
- SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions.Computational and structural biotechnology journal · 2023Article
- Filling gaps in metabolism using hypothetical reactions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Metabolite annotation from knowns to unknowns through knowledge-guided multi-layer metabolic networking.Nature communications · 2022Article
- Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx.Nature communications · 2022Article
- 15 years of microbial biotechnology: the time has come to think big-and act soon.Microbial biotechnology · 2022Article
- NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism.eLife · 2021Article
- A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives.Nature communications · 2021Article
- PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models.STAR protocols · 2021Article
- Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome biology · 2021Review
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
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 ∼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-databases.epfl.ch/atlas.
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