geWorkbench

Overview

SkyBase is a database that stores the homology models built by SkyLine analysis for all NESG PSI2 protein structures. Users can search the database with their sequence of interest to find homology models which meet user-defined alignment coverage and sequence identity constraints.

SkyBase Tutorial

http://skybase.c2b2.columbia.edu/nesg3/help/help.html

Database Search Page

http://skybase.c2b2.columbia.edu/nesg3/nesg.php

SkyBase in geWorkbench

After query with the sequence for PDB file 1e09:

Note on column sorting

In the initial display, the data is sorted in descending order on the second column, "Id% query-model-sequence". If any column header is clicked, the data table will be resorted on that column in three successive ways with repeated clicks.

• Original order (column 2, descending)
• Ascending order
• Descending order

Detail, upper left

Detail, upper right

VAT page

VAQ page

References

Lee H, Li Z, Silkov A, Fischer M, Petrey D, Honig B, Murray D. (2010) High-throughput computational structure-based characterization of protein families: START domains and implications for structural genomics. J Struct Funct Genomics. 11(1):51-9. Link to paper

Mirkovic N., Li Z., Parnassa A., Murray D. (2007) Strategies for High-Throughput Comparative Modeling: Applications to Leverage Analysis in Structural Genomics and Protein Family Organization. Proteins: Structure, Function, and Bioinformatics 66:766-777.