Blobulation is an approach for edge-detection in protein sequences based on contiguous hydrophobicity, which we originally developed for a specific long intrinsically disordered protein (the prodomain of BDNF).
The blobulator is a webtool for blobulation, which allows the user to blobulate any sequence, and visualize the results while adjusting the two blobulation parameters to detect more edges for higher-resolution (“zooming-in”) or detect fewer edges for a more tractable visualization (“zooming-out”).
Collaborative work with the Cheng lab at Washington University-St Louis was just published in eLife! “Polyunsaturated fatty acids inhibit a pentameric ligand-gated ion channel through one of two binding sites” used photolabeling and Mark’s coarse-grained MD simulations to identify two binding sites for polyunsaturated fatty acids (DHA), and functional studies with modifications to determine which site is responsible for the effects of DHA. This paper also provided another test of the method for lipid affinities from density distributions that we published here.