• Multiple Alignment Generator - Generate homology sequences based on Blastp's result, then reduces the redundant sequences by CD-hit or taxonomy information, finally, run Clustalw to generate Multiple Sequences Alignment. Also user can reselect the sequences in the result set or based on taxonomy report.
• Motif Maker - Identify the conserved continuous residues segment,  motif,  which that can be used for experimental mutational design to analyze function of a protein family.
• Motif Search / Sequence DB - Identify structural and functionally related sequences that share similar motifs.
• Motif Search / Single Sequence - Based on family  motif profile , find the motifs in a query sequence.
• SVP Visualization - 3D images of protein structures colored according to variability, as determined by PCPMer,  can be used to visualize residues conserved in their physical chemical properties (PCPs) 
• Sequence comparison to Motif DB-  Search motifs database to find related motifs with the query sequence. (Under Construction)
• Search for Motif in Motif DB - Search motifs database to find related motifs with  the query motif. (Under Construction)

A few of PCPMer applications can be found at AutoMotif(PCPMer Motif Management System). We are constructing databases of motifs for function related protein, such as Allergen, Titin,....(Web site is under Construction)

• Info of PCPMer
  • Try New version of PCPMer
  • Web Application (2005 version)
  • Standalone Version (2005 version)
• Authors
  • Bin Zhou
  • Fabian Braun
  • Catherine H. Schein
  • Werner Braun
• 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 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