Families of Structurally Similar Proteins or FSSP is a
database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...
of structurally superimposed proteins generated using the "Distance-matrix ALIgnment" (DALI)
algorithm
In mathematics and computer science, an algorithm () is a finite sequence of Rigour#Mathematics, mathematically rigorous instructions, typically used to solve a class of specific Computational problem, problems or to perform a computation. Algo ...
.The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (remote homologs, < 30% sequence identity), as well as all structures in the Protein Data Bank with 70-30% sequence identity relative to the search structure (medium homologs). Very close homologs (above 70% sequence identity) are excluded as they rarely have marked structural differences. The alignments of remote homologs are the result of pairwise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based purely on the 3D co-ordinates of the proteins and are derived by automatic (objective) structure comparison programs. The significance of structural similarity is estimated based on statistical criteria. The FSSP database is available electronically from the EMBL file server and by anonymous ftp (file transfer protocol).
The database is helpful for the comparison of
protein structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid ...
s.
See also
*
CATH Cath may refer to:
__NOTOC__ People
* Cath Bishop (born 1971), British former rower and 2003 world champion
* Cath Carroll (born 1960), British musician and music journalist
* Cath Coffey (), one of the earliest members of British rap band Stereo ...
*
SCOP
A ( or ) was a poet as represented in Old English poetry. The scop is the Old English counterpart of the Old Norse ', with the important difference that "skald" was applied to historical persons, and scop is used, for the most part, to designat ...
References
External links
FSSP Search page at EBI
Protein structure
Protein classification
Protein databases
Protein superfamilies
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