AIMC Topic: Biosynthetic Pathways
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Applications of artificial intelligence to enzyme and pathway design for metabolic engineering.
Current opinion in biotechnology
Aug 3, 2021
Metabolic engineering for developing industrial strains capable of overproducing bioproducts requires good understanding of cellular metabolism, including metabolic reactions and enzymes. However, metabolic pathways and enzymes involved are still unk...
Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits.
Journal of chemical information and modeling
Jul 12, 2021
The central challenge in automated synthesis planning is to be able to generate and predict outcomes of a diverse set of chemical reactions. In particular, in many cases, the most likely synthesis pathway cannot be applied due to additional constrain...
A deep learning approach to evaluate the feasibility of enzymatic reactions generated by retrobiosynthesis.
Biotechnology journal
Jan 18, 2021
Retrobiosynthesis allows the designing of novel biosynthetic pathways for the production of chemicals and materials through metabolic engineering, but generates a large number of reactions beyond the experimental feasibility. Thus, an effective metho...
Classification of alkaloids according to the starting substances of their biosynthetic pathways using graph convolutional neural networks.
BMC bioinformatics
Jul 9, 2019
BACKGROUND: Alkaloids, a class of organic compounds that contain nitrogen bases, are mainly synthesized as secondary metabolites in plants and fungi, and they have a wide range of bioactivities. Although there are thousands of compounds in this class...
CGPS: A machine learning-based approach integrating multiple gene set analysis tools for better prioritization of biologically relevant pathways.
Journal of genetics and genomics = Yi chuan xue bao
Sep 13, 2018
Gene set enrichment (GSE) analyses play an important role in the interpretation of large-scale transcriptome datasets. Multiple GSE tools can be integrated into a single method as obtaining optimal results is challenging due to the plethora of GSE to...
Enhancement of Nucleoside Production in Based on Biosynthetic Pathway Analysis.
BioMed research international
Nov 29, 2017
To enhance nucleoside production in , the biosynthetic pathways of purine and pyrimidine nucleosides were constructed and verified. The differential expression analysis showed that , and genes involved in purine nucleotide biosynthesis were signifi...
Selected essential oils inhibit key physiological enzymes and possess intracellular and extracellular antimelanogenic properties in vitro.
Journal of food and drug analysis
Apr 20, 2017
Essential oils (EOs) extracted from six medicinal herbs and food plants [Cinnamomum zeylanicum (CZ), Psiadia arguta (PA), Psiadia terebinthina (PT), Citrus grandis (CGp), Citrus hystrix (CH), and Citrus reticulata (CR)] were studied for any inhibitor...
IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.
mBio
Jul 14, 2015
UNLABELLED: In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In...
Molecular insights fast-tracked: AI in biosynthetic pathway research.
Natural product reports
May 22, 2025
Covering: 2000 to 2025This review explores the potential of artificial intelligence (AI) in addressing challenges and accelerating molecular insights in biosynthetic pathway research, which is crucial for developing bioactive natural products with ap...
Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model.
Nucleic acids research
Apr 10, 2025
Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC predict...
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