Babbitt Lab > Resources > Supplementary data from "T. brucei and human degradomes: a global comparison of sequences and structures"

T. brucei and Homo sapiens predicted active protease resource

T. brucei and human degradomes: a global comparison of sequences and structures

Mashiyama, ST, Babbitt, PC, McKerrow, JH, 2010, in preparation

Abstract: Rational drug design efforts are aided by knowledge of the sequence and structure of drug targets, and their homologs. We have performed a genome-level computational study of sequence and structure similarities using crystal structures and models of the proteases of Homo sapiens and a human pathogen Trypanosoma brucei. This global resource enables a survey of the degradome landscapes of these two species, facilitating comparisons and proffering clues for drug design. Several groups of proteases are examined in detail, providing both new insights about their potential usefulness as targets, and the value of this global approach in mining new pathogen genomes as they become available.

Network views show similarity relationships. The figure to the left shows structure similarities between T. brucei and human proteases that have crystal structures or reliable models.
Parasite proteases: triangles;
Human: round.

Network views may be viewed and manipulated
with the program Cytoscape available here:
Cytoscape home page

A basic tutorial in using network files and navigating in Cytoscape has been posted by a former Babbitt lab member here:
Basic Cytoscape tutorial

Network, sequence, and structure data files

Data file Description
TbHs_fast_SN4.5.cys Cytoscape network file of structure relationships between human and T. brucei proteases.
TbHs_bst_1eNeg5_bst.cys Cytoscape network file of sequence similarity relationships between human and T. brucei proteases
active T. brucei proteases T. brucei protein sequences, trimmed to peptidase regions, fasta formatted
active human proteases Human protein sequences, from MEROPS peptidase sequences and other human sequences trimmed to peptidase domains, as described, fasta formatted.
TbHs_pdbs_models_all_trimmed.tgz T. brucei and human PDB and model files, trimmed to peptidase regions
T. brucei curation data Data used for evidence in identifying T. brucei active proteases