RetroBioCat Database: A Platform for Collaborative Curation and Automated Meta-Analysis of Biocatalysis Data

Abstract

Despite the increasing use of biocatalysis for organic synthesis, there are currently no databases that adequately capture synthetic biotransformations. The lack of a biocatalysis database prevents accelerating biocatalyst characterization efforts from being leveraged to quickly identify candidate enzymes for reactions or cascades, slowing their development. The RetroBioCat Database (available at retrobiocat.com) addresses this gap by capturing information on synthetic biotransformations and providing an analysis platform that allows biocatalysis data to be searched and explored through a range of highly interactive data visualization tools. This database makes it simple to explore available enzymes, their substrate scopes, and how characterized enzymes are related to each other and the wider sequence space. Data entry is facilitated through an openly accessible curation platform, featuring automated tools to accelerate the process. The RetroBioCat Database democratizes biocatalysis knowledge and has the potential to accelerate biocatalytic reaction development, making it a valuable resource for the community.

Multienzymatic Cascades and Nanomaterial Scaffolding—A Potential Way Forward for the Efficient Biosynthesis of Novel Chemical Products

“…We do note the establishment of an initial retrobiosynthetic framework in the form of the RetroBioCat Database. [ 217,218 ] In line with this we also note the establishment of preliminary standards for reporting such biocatalytic data in the form of the Standards for Reporting Enzymology Data (STRENDA) database, which incorporates guidelines and recommendations for scientific journal publications. [ 219 ]…”

Biocatalysis: landmark discoveries and applications in chemical synthesis

“…Computer-aided synthesis planning (CASP) has revolutionised retrosynthetic analyses, using computers to automate the process, learning from literature sources and databases of organic reactivity and experimental reaction, to create potential synthetic routes towards targets. RetroBioCat is a powerful CASP tool enabling retrosynthetic analysis for the design of biocatalytic reactions and cascades, 116,117 an area other retrosynthetic databases does not sufficiently depict. RetroBioCat uses programmed reaction rules and encoded potential biocatalysts with their associated substrate specificity's, to automate the synthetic biotransformation design process.…”

Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants

“…However, P450 monooxygenases were excluded from the RetroBioCat Database. 67 This article is licensed under CC-BY-NC-ND 4 Here, we present a complete and current overview of P450 BM3 variants and their catalyzed reactions. This review conveniently associates each P450 BM3 variant with its corresponding catalyzed reaction, including hydroxylation, epoxidation, carbene transfer, and more, in the form of a database, available as Supplementary Table 1.…”

“…We determined that a database would provide the optimal means to categorize this knowledge and, most importantly, to enable extraction of information. The Turner lab recently presented the RetroBioCat Database, which serves as a platform for synthetic biotransformations . The database is highly recommended for researchers who are unfamiliar with enzymes but are considering using them for synthetic transformations.…”