Abstract: FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank. (PDB) (1). The current release. PDF | FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB). The database currently. FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB) . The database currently .
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The results of the exhaustive pairwise structure comparisons are reported in the form of a fold tree generated by hierachical clustering and as a series of structurally representative sets of folds at varying levels of uniqueness. For each query structure from the representative set, there is a database entry containing structure-structure alignments with its structural neighbours in the representative set and its sequence homologs in the PDB.
All alignments are based purely on the 3-D co-ordinates of the proteins and are derived by an automatic structure comparison program Dali.
Most newly determined protein sequences can be classified into families by sequence homology. However, protein families are known to catabase the shape of the fold even when sequences have diverged below the limit of detection of significant similarities at the sequence level.
These similarities can be detected by structural comparisons that merge protein families of daatabase 3-D structure into structural classes, the members of which may or may not be evolutionarily related 1—4.
The FSSP database of structurally aligned protein fold families.
The FSSP database contains a fold classification based on exhaustive structural alignments of known structures. The database databwse a rich source of information for the study of both divergent and convergent aspects of the evolution of protein folds and defines useful test sets and a standard of truth for assessing the correctness of sequence-sequence or sequence-structure alignments.
The major new developments since last year 5 are continuous updates fsps the database and easy access to the data using browsers on the World Wide Web WWW. The sequence-representative set is derived using algorithm 1 of ref. As expected from the high sequence identity, the folds of both of the 1AAP chains and that of 9PTI are as good as identical 1.
This set includes many pairs of remote homologs that have completely superimposable 3-D structures despite low sequence similarity and pairs with recurrent common folding motifs. The sequence-representative set is clustered further based on all-against-all structure comparison within the sequence-representative set. The tree gives a simple overview of protein families, grouping together remote homologs and joining topologically similar but not necessarily evolutionarily related proteins in the lower branches.
For example, Figure 2 shows how dagabase first C2 domain of synaptotagmin I PDB entry 1RSYwhich presented a new calcium-binding fold 7is firmly anchored in a large structural class that contains beta-sandwich proteins with topological similarity to immunoglobulin-like domains and blue copper proteins. An alternative way of defining clusters in protein fold space is used to derive the PDBfolds series of structurally representative sets using algorithm 2 of ref.
The sets of representative folds contain a maximal number of protein folds where no pair is allowed to have a larger fraction of structurally equivalent residues than a given threshold percentage.
This reduces the number of unique folds to consider for structural analysis, depending on the threshold chosen.
Finding proteins in FSSP. The index can be used for searching by protein name or PDB code. In this example, 31 PDB chains clustered into the sequence family represented by bovine pancreatic trypsin inhibitor fatabase have been extracted from the table.
For each protein chain in the representative set, with PDB identifier Nxxx like: FSSP which contains a few or tens of proteins structurally similar to the search structure, alongside the secondary structure and solvent accessibility extracted from the 3-D coordinates of the search structure 8. Details about the Dali method used to derive the database are given in refs 9 and An FSSP file datwbase divided in five formatted blocks and a free text footer which explains the format.
See below for automatic parsing of FSSP entries. FSSP entries are parsed on the fly to display structural neighbours of individual proteins in the form of structure alignments fsdp out horizontally, multiple structure alignments known structures combined with multiple sequence alignments [sequences homologous to a known structure: There are further hypertext links to functional annotations and literature references via SRS These patterns are conserved darabase all members of the protein families as seen by extending the structure alignment with the results from a sequence database search Clicking on the sequence identifier e.
Overview of protein fold space.
The FSSP database of structurally aligned protein fold families.
Plotted with WhatIf The FSSP data sets can be obtained by anonymous ftp from ftp. Academic redistribution of single files or of the entire database is fss.
No inclusion in other databases or database services, academic or other, without explicit permission of the authors. Not to be used for classified research.
Users are asked to refer to ref. Fssl current database contains at most one alignment per pair of full length proteins. The alignments are constrained to be sequential as this is fsap meaningful though not imposed by the Dali method. The structure comparison program Dali 9 defines the extent of the common structural core by maximizing the agreement of intra molecular CA-CA distances.
The scoring function was deliberately designed to allow inter-domain conformational flexibility; hence, positional root mean square deviations for the corresponding rigid-body superimpositions are often higher than for comparison methods that put an absolute upper limit on inter molecular positional deviations.
This, however, is only an apparent disadvantage. Combining multiple structure-structure alignments with multiple sequence-sequence alignments.
A multiple sequence alignment of four protein families: Only structurally equivalent blocks are shown; the middle part of the alignment has been omitted in order to highlight the conserved sequence signatures near the N- and C-termini. Structural alignment defines the register of each of the families indicated in the FSSP column relative to p21 ras. In addition to the guide structures, the alignment includes representative sequence homologs Swissprot column; first sequence corresponds to the known structure taken from the HSSP database of sequence-sequence alignments For example, the original HSSP entry for 5p21 lists sequences; here, only 29 representativeras sequences are shown.
More information on the Dali server 10 is available on the WWW at: Kindly report any problems to the authors by e-mail. Oxford University Press is a department of the University of Oxford.
It furthers the University’s objective fswp excellence in research, scholarship, and education by publishing worldwide.
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