webPIPSA

Protein Interaction Property Similarity Analysis

• Home
• Run PIPSA
• Documentation
• Demonstration
• Download
• References
• Funding
• Project
  Information
• Imprint
  Privacy
• Terms and Conditions

qPIPSA Parameter Retrieval and Estimation Module

What this module does?

1. Retrieval of relevant parameters and associated information from BRENDA and SABIO-RK, as well as protein sequences from UNIPROT and protein structures from PDB, MODBASE and SWISSMODEL
2. Parameter estimation using available protein structure information. Currently the PIPSA method is used to do this. PIPSA analysis can be used to aid the estimation of kinetic parameters from a similarity analysis of the electrostatic potentials of the enzyme for which the parameter is needed and the enzymes for which parameters are already known.
3. A list of CHANGES can be found here

For more information on the use of this module click here.

Retrieval of parameters and related information

This is based on insertion of a unique protein identifier. Currently a UNIPROT accession code must be given. The workflow depends on an EC annotation in the description line of your UNIPROT entry. Alternatively you can provide the EC annotation together with the UNIPROT accesssion (seperated by a colon). This EC link is used to search in BRENDA and SABIO-RK entries.

Please enter :
	UNIPROT accession code together with an EC number (eg. P35520:4.2.1.22) [?]
	a valid email address [?]

In case of unknown or only vaguely known protein functionality ProFAT may assist in detecting protein function and structural homology.

http://cluster-1.mpi-cbg.de/profat/profat.html

ProFAT is a tool for the functional annotation of proteins via the detection of weak homologies. Sequence homology is detected with NCBI's PSI-BLAST system. Structural homology is detected with UCL's Threader software. These results are then combined by the use of GenBank annotation and basic text mining.

ProFAT requires the user to submit a keyword list along with the protein sequence. Several pre-made keyword lists are available, however, the system is used optimally with a user defined keyword list consisting of suspected or experimentally determined information.

Bradshaw C. R., Surendranath V., and Habermann B. BMC Bioinformatics 2006, 7:466