In this Project , we develop method to automatically detect motifs in a protein family and subsequently identifies related members in protein sequence database. The tool calculates conservation of PCP descriptors, quantitative descriptors for amino acids based on multi-dimensional scaling of 237 physical-chemical properties, to define a motif. Each motif is described as profile that consists of average vector magnitude, standard deviation and relative entropy. Applications of PCPMer includes:
1. Identification of conserved residues, motifs that can be used for experimental mutational design to analyze function of a protein family.
2. To identify structural and functionally related sequences that share similar motifs.
3. For large-scale datamining and annotation of translated genomic sequences
The developement of PCPMer software is supported by the U.S. Department of Energy (DE-FG-00ER63041), a Research Development Grant (#2535-01) from the John Sealy Memorial Endowment Fund for Biomedical Research, and by FDA Grant FD-U-002249-1.