HSSP curve

From Protein Prediction 2 Winter Semester 2014
Revision as of 11:32, 20 November 2014 by Ppwikiuser (talk | contribs)

Introduction to HSSP curve?

HSSP is a derived database merging structural (3-D) and sequence (1-D) information. For each protein of known 3-D structure from the Protein Data Bank (PDB), the database has a multiple sequence alignment of all available homologues and a sequence profile characteristic of the family. The list of homologues is the result of a database search in SwissProt using a position-weighted dynamic programming method for sequence profile alignment (MaxHom). The database is updated frequently. The listed homologues are very likely to have the same 3-D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of aligned sequence families, but also a database of implied secondary and tertiary structures covering 29% of all SwissProt-stored sequences.


Different thresholds for HSSP-curve
Different thresholds for HSSP-curve


Existing visualisations

Core Functionalities

Progress

Task Implemented
Core Functionality No
Drag nodes No
Display additional info on mouse-over No
Edit graph and export changes No
PBseq format compatibility No
Connect (.ct) format compatibility No

People

References

http://en.wikipedia.org/wiki/Homology-derived_Secondary_Structure_of_Proteins

http://www.ncbi.nlm.nih.gov/pubmed/?term=UniqueProt%3A+creating+representative+protein+sequence+sets

http://en.wikipedia.org/wiki/Protein_superfamily

http://nar.oxfordjournals.org/content/24/1/201.full.pdf