SCOP database in 2004: refinements integrate structure and sequence family data - PubMed (original) (raw)

SCOP database in 2004: refinements integrate structure and sequence family data

Antonina Andreeva et al. Nucleic Acids Res. 2004.

Abstract

The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are hierarchically classified into families, superfamilies, folds and classes. The continual accumulation of sequence and structural data allows more rigorous analysis and provides important information for understanding the protein world and its evolutionary repertoire. SCOP participates in a project that aims to rationalize and integrate the data on proteins held in several sequence and structure databases. As part of this project, starting with release 1.63, we have initiated a refinement of the SCOP classification, which introduces a number of changes mostly at the levels below superfamily. The pending SCOP reclassification will be carried out gradually through a number of future releases. In addition to the expanded set of static links to external resources, available at the level of domain entries, we have started modernization of the interface capabilities of SCOP allowing more dynamic links with other databases. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.

PubMed Disclaimer

Similar articles

• SCOP database in 2002: refinements accommodate structural genomics.
  Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. Lo Conte L, et al. Nucleic Acids Res. 2002 Jan 1;30(1):264-7. doi: 10.1093/nar/30.1.264. Nucleic Acids Res. 2002. PMID: 11752311 Free PMC article.
• Data growth and its impact on the SCOP database: new developments.
  Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. Andreeva A, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D419-25. doi: 10.1093/nar/gkm993. Epub 2007 Nov 13. Nucleic Acids Res. 2008. PMID: 18000004 Free PMC article.
• The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures.
  Andreeva A, Kulesha E, Gough J, Murzin AG. Andreeva A, et al. Nucleic Acids Res. 2020 Jan 8;48(D1):D376-D382. doi: 10.1093/nar/gkz1064. Nucleic Acids Res. 2020. PMID: 31724711 Free PMC article.
• The SUPERFAMILY database in structural genomics.
  Gough J. Gough J. Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1897-900. doi: 10.1107/s0907444902015160. Epub 2002 Oct 21. Acta Crystallogr D Biol Crystallogr. 2002. PMID: 12393919 Review.
• Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling.
  Andreeva A. Andreeva A. Biochem Soc Trans. 2016 Jun 15;44(3):937-43. doi: 10.1042/BST20160053. Biochem Soc Trans. 2016. PMID: 27284063 Free PMC article. Review.

Cited by

• Biochemical and crystallographic studies of L,D-transpeptidase 2 from Mycobacterium tuberculosis with its natural monomer substrate.
  de Munnik M, Lang PA, Calvopiña K, Rabe P, Brem J, Schofield CJ. de Munnik M, et al. Commun Biol. 2024 Sep 18;7(1):1173. doi: 10.1038/s42003-024-06785-3. Commun Biol. 2024. PMID: 39294212 Free PMC article.
• Intrinsic disorder may drive the interaction of PROS1 and MERTK in uveal melanoma.
  Djulbegovic M, Taylor Gonzalez DJ, Antonietti M, Uversky VN, Shields CL, Karp CL. Djulbegovic M, et al. Int J Biol Macromol. 2023 Oct 1;250:126027. doi: 10.1016/j.ijbiomac.2023.126027. Epub 2023 Jul 26. Int J Biol Macromol. 2023. PMID: 37506796 Free PMC article.
• Nucleolar- and Nuclear-Stress-Induced Membrane-Less Organelles: A Proteome Analysis through the Prism of Liquid-Liquid Phase Separation.
  Mokin YI, Gavrilova AA, Fefilova AS, Kuznetsova IM, Turoverov KK, Uversky VN, Fonin AV. Mokin YI, et al. Int J Mol Sci. 2023 Jul 2;24(13):11007. doi: 10.3390/ijms241311007. Int J Mol Sci. 2023. PMID: 37446185 Free PMC article.
• Biomolecular condensates: insights into early and late steps of the HIV-1 replication cycle.
  Di Nunzio F, Uversky VN, Mouland AJ. Di Nunzio F, et al. Retrovirology. 2023 Apr 7;20(1):4. doi: 10.1186/s12977-023-00619-6. Retrovirology. 2023. PMID: 37029379 Free PMC article. Review.
• Virulence network of interacting domains of influenza a and mouse proteins.
  Ng TA, Rashid S, Kwoh CK. Ng TA, et al. Front Bioinform. 2023 Feb 17;3:1123993. doi: 10.3389/fbinf.2023.1123993. eCollection 2023. Front Bioinform. 2023. PMID: 36875146 Free PMC article.

References

1. 1. Murzin A., Brenner,S.E., Hubbard,T.J.P. and Chothia,C. (1995) SCOP: a Structural Classification of Proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536–540. - PubMed
2. 1. Brenner S.E., Chothia,C., Hubbard,T.J.P. and Murzin,A. (1996) Understanding protein structure: using SCOP for fold interpretation. Methods Enzymol., 266, 635–643. - PubMed
3. 1. Bernstein F.C., Koetzle,T.F., Williams,G.J.B., Meyer,E.F., Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535–542. - PubMed
4. 1. Westbrook J., Feng,Z., Jain,S., Bhat,T.N., Thanki,N., Ravichandran,V., Gilliland,G.L., Bluhm,W., Weissig,H., Greer,D.S. et al. (2002) The Protein Data Bank: unifying the archive. Nucleic Acids Res., 30, 245–248. - PMC - PubMed
5. 1. Lo Conte L., Brenner,S.E., Hubbard,T.J.P., Chothia,C. and Murzin,A.G. (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res., 30, 264–267. - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Europe PubMed Central
  • Ovid Technologies, Inc.
  • PubMed Central
  • Silverchair Information Systems

• Research Materials

  • NCI CPTC Antibody Characterization Program