Download DReSPat package   |   Readme   |  

DReSPat program is supported currently on Linux. It has command line interface. The input to DReSPat is a set of PDB files and output is the recurring functional sites in the given set of proteins. To know more about DReSPat, read our paper in Journal of Molecular Biology. DReSPat employs graph theoretic detection of recurring functional sites. The functional site is modelled as a clique, detection of which is a time consuming process. Besides that it is not scalable beyond a certain number of proteins. The results of DReSPat were compiled by detecting recurring functional sites from the proteins beloging to the same SCOP superfamily.

To alleviate the problems in DReSPat, we have employed geometric invariant techniques. Geometric Invariant approach provides far richer result set than that of DReSPat. It also uncovers novel relationships between superfamilies and patterns at protein-protein interface. Click here to download programs and view results obtained with geometric invariant approach of functional site detection in proteins.

Pramod P. Wangikar, Ashish V. Tendulkar, S. Ramya, Deepali N. Mali and Sunita Sarawagi, Functional Sites in Protein Families Uncovered via an Objective and Automated Graph Theoretic Approach, Journal of Molecular Biology, Volume 326, Issue 3, , 21 February 2003, Pages 955-978.

1. Download PDB files in which we want to find recurring structural patterns from www.rcsb.org.
2. Run perl start.pl. It gives a set of options to run either entire DReSPat or PDB parser or pattern finder. Read readme file for more details.