RadicalSAM.org enables the use of the EFI's genomic enzymology web tools for studies of the radical SAM superfamily (RSS) by providing:
1 - UniProt accession IDs for the members of the 20 functionally characterized subgroups curated by the Structure-Function Linkage Database (SFLD) as well as subgroups without characterized functions. The IDs are updated with each release of the UniProt and InterPro databases (every 8 weeks).
The IDs can be used as the input for Option D of EFI-EST to generate sequence similarity networks (SSNs). The SSNs are used for exploring sequence-function space and, also as input, to discover genome context using EFI-GNT and human microbiome metagenome abundance using EFI-CGFP. In contrast to the SSN for the entire, extremely large RSS, the SSNs for the smaller subgroups can be analyzed with Cytoscape using most laptop/desktop computers.2 - Multiple sequence alignments (MSAs), WebLogos, hidden Markov models (HMMs), length histograms, phylogenetic distribution, and conservation of user-defined residues for the subgroups to aid inference of reactions and mechanisms.
3 - Community-provided lists of experimentally characterized functions to supplement the annotations curated by SwissProt.
4 - Community-updated lists of publications.
A stride in making biological big data analysis more transparent, accessible and 'democratic'. This particular dataset, the radical SAM protein superfamily, is massive and requires a notable amount of computational power to analyze in a network format; resources like this make these datasets more available and tangible to researchers of a wide range of computational capabilities.
User interface is appealing and easy to use; manipulation of the dataset takes a little practice and knowing what you want to examine prior to navigating the site and its features.