Quick Look

FSSP is both known as Fold classification based on Structure-Structure alignment of Proteins and Families of Structurally Similar Proteins. The FSSP classification scheme is based on an exhaustive 3D structure comparison of protein structures in the Protein Data Bank. Alignments and classification are done automatically and are updated continuously by the Dali search engine.  

Classification Scheme

DALI - Dali stands for Distance matrix ALIgnment. Dali is an automatic server that does a 3D comparison of protein structures. The output of the Dali server is the query structure and a corresponding multiple sequence-structure alignment of similarly structured proteins.

The Protein chains are divided into two: a representative set of chains and a set of sequence homologs for each representative chain. "Sequence homologs have more than 25% sequence identity, and the representative set contains no pair of such sequence homologs. An all-against-all structure comparison is performed on the representative set. The resulting alignments are reported in the FSSP entries for individual chains." (http://www2.ebi.ac.uk/dali/fssp/)

Each FSSP entry includes the structure alignments of the search structure with its sequence homologs. Classification and Structure Alignments are continuously updated when new structures are available at the Protein Data Bank.

Compared to other classification databases, FSSP is unique in that it employs a purely automated method of classification.

For sample Sequence and Structure Alignments using Dali, please go to the "Particular Peroxidases" section of this presentation.