• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of prosciprotein sciencecshl presssubscriptionsetoc alertsthe protein societyjournal home
Protein Sci. Dec 1992; 1(12): 1691–1698.
PMCID: PMC2142138

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% 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.(ABSTRACT TRUNCATED AT 250 WORDS)

Full Text

The Full Text of this article is available as a PDF (822K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Abagyan RA, Maiorov VN. A simple qualitative representation of polypeptide chain folds: comparison of protein tertiary structures. J Biomol Struct Dyn. 1988 Jun;5(6):1267–1279. [PubMed]
  • Alexandrov NN, Takahashi K, Go N. Common spatial arrangements of backbone fragments in homologous and non-homologous proteins. J Mol Biol. 1992 May 5;225(1):5–9. [PubMed]
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. [PubMed]
  • Bork P, Sander C, Valencia A. An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7290–7294. [PMC free article] [PubMed]
  • Fischer D, Bachar O, Nussinov R, Wolfson H. An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins. J Biomol Struct Dyn. 1992 Feb;9(4):769–789. [PubMed]
  • Gotoh O. An improved algorithm for matching biological sequences. J Mol Biol. 1982 Dec 15;162(3):705–708. [PubMed]
  • Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Protein Sci. 1992 Mar;1(3):409–417. [PMC free article] [PubMed]
  • Holmgren A, Bränden CI. Crystal structure of chaperone protein PapD reveals an immunoglobulin fold. Nature. 1989 Nov 16;342(6247):248–251. [PubMed]
  • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. [PubMed]
  • Lesk AM, Brändén CI, Chothia C. Structural principles of alpha/beta barrel proteins: the packing of the interior of the sheet. Proteins. 1989;5(2):139–148. [PubMed]
  • Mitchell EM, Artymiuk PJ, Rice DW, Willett P. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J Mol Biol. 1990 Mar 5;212(1):151–166. [PubMed]
  • Overington J, Johnson MS, Sali A, Blundell TL. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc Biol Sci. 1990 Aug 22;241(1301):132–145. [PubMed]
  • Pascarella S, Argos P. A data bank merging related protein structures and sequences. Protein Eng. 1992 Mar;5(2):121–137. [PubMed]
  • Rao ST, Rossmann MG. Comparison of super-secondary structures in proteins. J Mol Biol. 1973 May 15;76(2):241–256. [PubMed]
  • Remington SJ, Matthews BW. A general method to assess similarity of protein structures, with applications to T4 bacteriophage lysozyme. Proc Natl Acad Sci U S A. 1978 May;75(5):2180–2184. [PMC free article] [PubMed]
  • Remington SJ, Matthews BW. A systematic approach to the comparison of protein structures. J Mol Biol. 1980 Jun 15;140(1):77–99. [PubMed]
  • Rossmann MG, Argos P. Exploring structural homology of proteins. J Mol Biol. 1976 Jul 25;105(1):75–95. [PubMed]
  • Sali A, Blundell TL. Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J Mol Biol. 1990 Mar 20;212(2):403–428. [PubMed]
  • Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 1991;9(1):56–68. [PubMed]
  • Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 1981 Mar 25;147(1):195–197. [PubMed]
  • Subbarao N, Haneef I. Defining topological equivalences in macromolecules. Protein Eng. 1991 Dec;4(8):877–884. [PubMed]
  • Taylor WR, Orengo CA. Protein structure alignment. J Mol Biol. 1989 Jul 5;208(1):1–22. [PubMed]
  • Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph. 1990 Mar;8(1):52–29. [PubMed]
  • Vriend G, Sander C. Detection of common three-dimensional substructures in proteins. Proteins. 1991;11(1):52–58. [PubMed]
  • Zuker M, Somorjai RL. The alignment of protein structures in three dimensions. Bull Math Biol. 1989;51(1):55–78. [PubMed]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...