The PoPS Programs

General PoPS Programs

The main PoPS program (JNLP program)
The new version of the original PoPS program. Use this module to create, edit and experiment with PoPS specificity models, and investigate and reason about individual substrate cleavage. This program is a JNLP/WebStart program. See here for help on how to install and use it.

Proteome Searching

Search a proteome - [Advanced search]
Search a whole proteome to find potential new targets for your protease. Requires a PoPS model. The advanced search allows filtering of predicted hits based on substrate accessibility, secondary structure and number of predicted sites.

Search a fasta file - [Advanced search]
Performs the same search as the proteome search, but within a set of proteins supplied in a fasta file. Requires a PoPS model. The advanced search allows filtering of predicted hits based on substrate accessibility, secondary structure and number of predicted sites.

Filter Proteome Hits
Filter output files from proteome searches, limiting by score thresholds and converting the results to html format that links to various databases such as PDB and NCBI.