PCPMer Project

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

Acknowledge

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.

Publications

• Schein, C.H., Zhou, B., Oezguen, N., Mathura, V.S., Braun, W., 2005, "Molego-based definition of the architecture and specificity of metal binding sites"  Proteins  58(1):200-210 [Abstract]    [Full Paper]
• Venkatarajan, M.S., Schein, C. H., Braun W., 2003, "Identifying physical chemical property based sequence motifs in protein families and superfamilies: Application to DNase I related endonuclease", Bioinformatics 19:1381-1390 [Abstract]    [Full Paper]
  
• Schein, CH , Ozgun N, Izumi T, Braun W. 2002, "Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases" BMC Bionformatics 3(1):37 [HTML]
  
• Venkatarajan, M.S. 2002, "Automated generation of sequence motifs and three dimensional models of proteins and their applications" UTMB Dissertation [HTML]
  
• Venkatarajan, M.S., Braun W., 2001, "New quantitative descriptors for amino acids based on multidimensional scaling of a large number of physical-chemical properties", J Mol Modeling 7:445-453 [HTML]   [PDF]   [Abstract]   [New Descriptors]