Justin S Diamond, Yang Zhang; THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes, Database, Volume 2018, Issue 1, 1 January 2018, bay090, https://doi.org/10.1093/database/bay090

Featured in OMICTOOLS at https://omictools.com/the-db-tool

THE-DB contains hard, medium, and easy threading protein targets for E. coli K12 and Human genomes.

Hard targets are characterized by none of the threading programs (Muster, Sparkx, and HHpred) being able to find a suitable template which is quantified by Z-score (6 for MUSTER, 7 for SPARKS-X, and 11 for HHSearch) Medium targets are those sequences in which only one or two of the threading programs finds a suitable template. Lastly, easy targets are those in which all threading programs find a suitable template.

The database allows column search filters, which can be changed by clicking on the corresponding filters.

The colored text indicates a link. Where blue sends the user to the Uniprot website for the clicked protein and red sends the user to the PDB counterpart.

By clicking on the Z-score of either three threading program, a 3D representation will pop up in color. Init.dat files can be downloaded by clicking on the download templates button. The threading output is the 20 top ranked templates which can be visualized by clicking on the corresponding numbers in the modal window after clicking the Z-Score column. By clicking on the show all templates button, a new page pops up that displays all 20 templates at once. By clicking on the show SA and pair constraints radio button the modal pops up with the fasta alignment for the query and template sequences, as well as the Solvent Accessibility profile and the pair constraints profile.

To search for specific sequences the user should identify the organism of interest, click "go browsing", and search by ID. In cases where no results, the sequence is not in our database.

Developed by Justin Sidney Diamond (pika pika PIKA)
email: j3tkd@bu.edu or justindiamondmusic@gmail.com