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Physical Chemical Property based Motif Analyzer
Web
Version Released Nov, 2005
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Based on conservation of PCP descriptors, quantitative descriptors for amino
acids based on multi-dimensional scaling of 237 physical-chemical properties,
PCPMer has a set of tools that can automatically detect motifs in a protein
family, subsequently identifies related members in protein sequence database or
family motif database and find the function sites on the surface.
- 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)
* User must register and sign in before using the PCPMer. If you have registration
already, please login
* If you have any question, please send us email