CPTC Reagents Data Portal

Databases

The µ Paraflo Biochip Technology developed by Dr. Xiaolian Gao is an in situ synthesis using an activation agent generated using digital light and conventional chemistry onto microfluidic microchip.  This unique m Paraflo system differs from conventional microarray in that it provides both a synthesis and assay platform.  The use of these high density peptide chips for protein assays performance is unique.  Current efforts are screening phosphoprotein binding proteins to develop clinical assays (diagnostic, prognostic and/or monitoring drug treatment).

The PepCyber database focuses primarily on the interactions between binding domains in phosphoprotein binding proteins (PPBPs) and phosphopeptides (PPEP). A procedure has been established for database and literature curation to populate PepCyber with information regarding the interactions between PPBD and their PPEP substrates which are mediated through SH2 domain binding. A user accessible version of the PepCyber web site (http://pepcyber.umn.edu/PepCyber) has been created. The database currently spans 111 human SH2 proteins containing 121 SH2 domains.  The phosphopeptide-protein interactions embedded in the database are divided into three categories which include established peptide-SH2 interactions, absence of a clear interaction but involvement of specific SH2 domain or SH2 protein.

Peptide array design wizard to assist with the design of a peptide chip has been established. The URL of this web site is http://micropepchip.umn.edu/microPepChip. This web server performs a five step array design, which includes a function that searches in PepCyber for a set of "seed sequences" of interest, and a group of "sequence writer" functions that produce derived sequences from the "seed sequences" based on the users’ requirements. Presently, four writer functions have been implemented, capable of producing N-terminal truncated sequences, C-terminal truncated sequences, and Ala-scan sequences. Moreover, three types of control sequences, where pY is replaced by Ala, Phe, or Tyr, respectively, are available.  The "peptide array design wizard" implemented in this version of the µ PepChip Pro server is able to guide the user through the procedure of peptide array design which includes: choosing replicate numbers, selecting seed sequences, writing derived sequences based on the seed sequence, and writing the array layout into a downloadable Excel table.