Skip to main content
PMC home page
Protein Science : A Publication of the Protein Society logoLink to Protein Science : A Publication of the Protein Society
. 1992 Mar;1(3):409–417. doi: 10.1002/pro.5560010313

Selection of representative protein data sets.

U Hobohm 1, M Scharf 1, R Schneider 1, C Sander 1
PMCID: PMC2142204  PMID: 1304348

Abstract

The Protein Data Bank currently contains about 600 data sets of three-dimensional protein coordinates determined by X-ray crystallography or NMR. There is considerable redundancy in the data base, as many protein pairs are identical or very similar in sequence. However, statistical analyses of protein sequence-structure relations require nonredundant data. We have developed two algorithms to extract from the data base representative sets of protein chains with maximum coverage and minimum redundancy. The first algorithm focuses on optimizing a particular property of the selected proteins and works by successive selection of proteins from an ordered list and exclusion of all neighbors of each selected protein. The other algorithm aims at maximizing the size of the selected set and works by successive thinning out of clusters of similar proteins. Both algorithms are generally applicable to other data bases in which criteria of similarity can be defined and relate to problems in graph theory. The largest nonredundant set extracted from the current release of the Protein Data Bank has 155 protein chains. In this set, no two proteins have sequence similarity higher than a certain cutoff (30% identical residues for aligned subsequences longer than 80 residues), yet all structurally unique protein families are represented. Periodically updated lists of representative data sets are available by electronic mail from the file server "netserv@embl-heidelberg.de." The selection may be useful in statistical approaches to protein folding as well as in the analysis and documentation of the known spectrum of three-dimensional protein structures.

Full Text

The Full Text of this article is available as a PDF (1.5 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2247–2249. doi: 10.1093/nar/19.suppl.2247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., 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. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  3. Heringa J., Argos P. Side-chain clusters in protein structures and their role in protein folding. J Mol Biol. 1991 Jul 5;220(1):151–171. doi: 10.1016/0022-2836(91)90388-m. [DOI] [PubMed] [Google Scholar]
  4. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. doi: 10.1002/bip.360221211. [DOI] [PubMed] [Google Scholar]
  5. Niefind K., Schomburg D. Amino acid similarity coefficients for protein modeling and sequence alignment derived from main-chain folding angles. J Mol Biol. 1991 Jun 5;219(3):481–497. doi: 10.1016/0022-2836(91)90188-c. [DOI] [PubMed] [Google Scholar]
  6. Orengo C. A., Taylor W. R. A rapid method of protein structure alignment. J Theor Biol. 1990 Dec 21;147(4):517–551. doi: 10.1016/s0022-5193(05)80263-2. [DOI] [PubMed] [Google Scholar]
  7. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Rooman M. J., Wodak S. J. Identification of predictive sequence motifs limited by protein structure data base size. Nature. 1988 Sep 1;335(6185):45–49. doi: 10.1038/335045a0. [DOI] [PubMed] [Google Scholar]
  9. Sander C., Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 1991;9(1):56–68. doi: 10.1002/prot.340090107. [DOI] [PubMed] [Google Scholar]
  10. Smith T. F., Waterman M. S. Identification of common molecular subsequences. J Mol Biol. 1981 Mar 25;147(1):195–197. doi: 10.1016/0022-2836(81)90087-5. [DOI] [PubMed] [Google Scholar]
  11. Taylor W. R., Orengo C. A. Protein structure alignment. J Mol Biol. 1989 Jul 5;208(1):1–22. doi: 10.1016/0022-2836(89)90084-3. [DOI] [PubMed] [Google Scholar]
  12. Unger R., Harel D., Wherland S., Sussman J. L. A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins. 1989;5(4):355–373. doi: 10.1002/prot.340050410. [DOI] [PubMed] [Google Scholar]
  13. Vriend G., Sander C. Detection of common three-dimensional substructures in proteins. Proteins. 1991;11(1):52–58. doi: 10.1002/prot.340110107. [DOI] [PubMed] [Google Scholar]

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

RESOURCES