Clusters of hydrophobic residues are known to promote structured protein stability and drive protein aggregation. In our recent work, identifying contiguous hydrophobic residue clusters within protein sequences (termed “blobs”) has been critical in interpreting intra-protein contacts in a series of intrinsically disordered protein simulations and defining the “local context” around disease-associated mutations across the human proteome. However, an accessible toolkit that identifies these clusters was unavailable, and the role that blobs play across the structural context of a variety of protein families remained unclear. Here, we present the blobulator toolkit, which consists of a webtool, a command line interface, and a VMD plugin. We demonstrate, in three example applications, how one might use the toolkit to identify blobs that reveal useful information about a globular protein, two orthologous membrane proteins, and an IDP. Finally, we present new features for the webtool, including the ability to view blobs on a protein structure via an interface to upload PDB files and integration of alphafold structures when using a UniProt ID. The blobulator webtool can be found at www.blobulator.branniganlab.org, and the source code with pip installable command line tool, as well as the VMD plugin with installation instructions, can be found on GitHub at https://github.com/BranniganLab/blobulator.
Pitman et al. (Sun,) studied this question.