MARTS-DB: a database of mechanisms and reactions of terpene synthases

BMC Bioinformatics. 2025 Dec 8. doi: 10.1186/s12859-025-06341-8. Online ahead of print.

ABSTRACT

BACKGROUND: Terpene synthases (TPSs) are enzymes that catalyze some of the most complex reactions in nature-the cyclizations of terpenes, which form the carbon backbones to the largest group of natural products, the terpenoids. On average, more than half of the carbon atoms in a terpene scaffold undergo a change in connectivity or configuration during these enzymatic cascades. Understanding TPS reaction mechanisms remains challenging, often requiring intricate computational modeling and isotopic labelling studies. Moreover, the relationship between TPS sequence and catalytic function is difficult to decipher, while data-driven approaches remain limited due to a lack of comprehensive, high-quality data sources. MAIN: We introduce the Mechanisms And Reactions of Terpene Synthases DataBase (MARTS-DB)-a manually curated, structured, and searchable database that integrates TPS enzymes, the terpenes they produce, and their detailed reaction mechanisms. MARTS-DB includes over 2850 reactions catalyzed by 1432 annotated enzymes from across all domains of life, with reaction mechanisms mapped as stepwise cascades for more than 500 terpenes. Accessible at https://www.marts-db.org, the database provides advanced search functionality and supports full dataset downloads in machine-readable formats. It also encourages community contributions to promote continuous growth.

CONCLUSION: User-friendly and comprehensive, MARTS-DB enables the systematic exploration of TPS catalysis, opening new avenues for computational analysis and machine learning, as recently demonstrated in the prediction of novel TPSs.

PMID:41361262 | DOI:10.1186/s12859-025-06341-8