Integration of sequence and reaction data for the design and engineering of SAM–dependent enzymes

We develop bioinformatics workflows based on the PyEED project and a research data management toolbox for biocatalytic data based on the EnzymeML project. In collaboration with the FOR 5596 project partners, the bioinformatics workflows are applied for studying sequence-function relationships, finding new enzyme candidates in sequence databases, and designing highly enriched mutant libraries. The research data management toolbox is based on the standardised data exchange format EnzymeML and is applied for managing, analysing, and publishing experimental and modelling results according to the FAIR data principles. The platform development is a collaborative project using existing tools such as GitHub, Jupyter, the Biopython library, and Galaxy, and incorporates existing databases, formats, and standards. The platform is used by all FOR 5596 partners, who will be enabled to install it locally, adapt it to their needs, and apply if for analysing and publishing their data and for sharing methods and results. The computational tools are reusable and extensible, the workflows enable reproducibility of data analysis, and the use of standardised formats make results interoperable. Thus, this project contributes to the digitalisation of (bio)catalytic sciences.