Comparison and classification of folding patterns from a database of protein structures is crucial to understand the principles of protein architecture, evolution and function. Current search methods for proteins with similar folding patterns are slow and computationally intensive. The sharp growth in the number of known protein structures poses severe challenges for methods of structural comparison. There is now a great need
for methods that can search the database of structures both accurately and rapidly.

We are researching for methods to search similar folding patterns using a concise tableau representation of proteins. Our contribution in this regard is summarized below:

1. We designed an approach that allows the extraction of identical and very closely-related protein folding patterns in constant-time.
2. We address the hard computational problem of extraction of maximally-similar subtableaux, when comparing two tableaux. We solve the problem using Quadratic programming and Integer Linear programming formulations and demonstrate their power to identify subtle structural similarities.
3. We developed a rapid method, TABLEAUSearch, for comparing a query structure against a database of protein domains, to identify structures with similar folding patterns. TABLEAUSearch is rapid enough to search the entire structural database in seconds on a standard desktop computer. Our new TABLEAUSearch server is now online!

Reference: A. S. Konagurthu, P. J. Stuckey, A. M. Lesk, Structural search and retrieval using tableau representation of protein folding patterns, Bioinformatics (in press).