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

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.