PCPMer 3.5.6

PCPMer is a software package for determining conserved regions in multiple sequence alignments. The software represents each of the 20 naturally occuring amino acids by five quantitative descriptors and can detect motifs (short regions of significant conservation) in aligned sequences based on relative entropy or physicochemical similarity. It can be then used to search for related proteins in a protein sequence database and map the variability data on a 3D structure (to make a stereophysicochemical variability plot, or SVP). Such plots are particularly useful for identifying the spatial relationships of highly conserved or variable residues to one another.

• Alignments - Generate multiple sequence alignments using the ClustalW program.
• Motif Maker - Identifies conserved segments ("motifs") in a multiple sequence alignment by means of the relative entropy (also known as the Kullback-Leibler divergence) or similarity of the sequences, when expressed in numerically in terms of five quantitative descriptors E1 to E5 (Venkatarajan and Braun, 2001). The program can work also incorporate user-defined descriptors.
  This information be used to identify likely functional areas, conserved epitopes, and to find more distant relatives of a protein family, using the following tools:
• Motif Search - Identify structural and functionally related sequences in a variety of databases that share similar motifs. The advantage of this approach is that motifs do not need to follow in the same order they occur in the sequence family that was used to define the motif list.
• 3D variability - 3D images of protein structures colored according to variability, as determined by PCPMer, can be used to visualize patches of residues conserved in their physical chemical properties, even if they come from different areas of the sequence.

• Authors (alphabetical order)
  • Braun, Fabian
  • Braun, Werner
  • Danecek, Petr
  • Garcia, Tzintzuni I.
  • Schein, Catherine H.
  • Mathura, Venkatarajan S.
  • Zhou, Bin
• References
  • Schein, C.H., Zhou, B. and Braun, W. Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses.
    Virol. J. Apr 21;2(1):40, 2005. [Abstract] [Full Paper]
  • 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]  
• Acknowledgements
  • The developement of PCPMer software is supported by the grants from the Food and Drug Administration (FDA HHSF223200710011I) and the National Institute of Health (NIH-R01-AI064913).