# The Blobulator: A Toolkit for Identification and Visual Exploration of Hydrophobic Modularity in Protein Sequences

## TL;DR

The Blobulator is a new toolkit for identifying and visualizing hydrophobic modules in protein sequences, offering web, plugin, and command line tools for analysis.

## Contribution

Introduces the Blobulator toolkit for hydrophobic module detection and visualization in proteins.

## Key findings

- Blobulator uses the blobulation algorithm to detect hydrophobic modules in proteins.
- The toolkit includes a webtool, VMD plugin, and command line interface for accessibility.
- Applications demonstrate its use in globular, membrane, and disordered proteins.

## Abstract

While contiguous subsequences of hydrophobic residues
are essential
to protein structure and function, as in the hydrophobic core and
transmembrane regions, there are no current bioinformatics tools for
module identification focused on hydrophobicity. To fill this gap,
we created the blobulator toolkit for detecting,
visualizing, and characterizing hydrophobic modules in protein sequences.
This toolkit uses our previously developed algorithm, blobulation,
which was critical in both interpreting intraprotein contacts in a
series of intrinsically disordered protein simulations (Lohia et al.,
2019) and defining the “local context” around disease-associated
mutations across the human proteome (Lohia et al., 2022). The blobulator toolkit provides accessible, interactive, and
scalable implementations of blobulation. These are available via a
webtool, a visual molecular dynamics (VMD) plugin, and a command line
interface. We highlight use cases for visualization, interaction analysis,
and modular annotation through three example applications: a globular
protein, two orthologous membrane proteins, and an intrinsically disordered
protein. 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 www.GitHub.com/BranniganLab/blobulator.