A database of protein structure families with common folding motifs

Abstract

The availability of fast and robust algorithms for protein structure comparison provides an opportunity to produce a database of three-dimensional comparisons, called families of structurally similar proteins (FSSP). The database currently contains an extended structural family for each of 154 representative (below 30% sequence identity) protein chains. Each data set contains: the search structure; all its relatives with 70-30'70 sequence identity, aligned structurally; and all other proteins from the representative set that contain substructures significantly similar to the search structure. Very close relatives (above 70% sequence identity) rarely have significant structural differences and are excluded. The alignments of remote relatives are the result of pairwise all-against-all structural comparisons in the set of 154 representative protein chains. The comparisons were carried out with each of three novel automatic algorithms that cover different aspects of protein structure similarity. The user of the database has the choice between strict rigid-body comparisons and comparisons that take into account interdomain motion or geometrical distortions; and, between comparisons that require strictly sequential ordering of segments and comparisons, which allow altered topology of loop connections or chain reversals. The data sets report the structurally equivalent residues in the form of a multiple alignment and as a list of matching fragments to facilitate inspection by three-dimensional graphics. If substructures are ignored, the result is a database of structure alignments of full-length proteins, including those in the twilight zone of sequence similarity. The database makes explicitly visible architectural similarities in the known part of the universe of protein folds and may be useful for understanding protein folding and for extracting structural modules for protein design. The data sets are available via Internet.

Soliton concepts and protein structure

“…These figures have not changed since the year 2008, indicating that the number of different protein conformations is quite limited and probably most of them have already been observed. Furthermore, the great success of SCOP, CATH and other approaches such as FSSP [4] in classifying the architecture of proteins is a manifestation that proteins are built in a modular fashion from a relatively small number of different components.…”

ProSeg: a database of local structures of protein segments

“…Compared to these databases, however, ProSeg possesses several distinctive features. Most of the taxonomic databases-such as SCOP [12], CATH [13] and FSSP [14]-accumulate data of domains, and not of short segments. In contrast to the domain-based databases, which are informative for understanding the divergent evolution of proteins, ProSeg, by focusing on short segments, may be helpful in shedding lights on the convergent evolution of proteins.…”

A new definition and properties of the similarity value between two protein structures

“…Examples of methods based on numerical techniques to predict structural information are: SCOP (Structural Classification of Proteins) [9,10], CATH (Class, Architecture, Topology and Homologous superfamily) [13], TM-SCORE [14,15], STRUCTAL software [16], FSSP (Families of Structurally Similar Proteins) [17] and DALILITE [18].…”