SCOP Database in 2002: Refinements Accommodate Structural Genomics

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2001 Dec 26

PMID 11752311

Citations 147

Authors

Loredana Lo Conte

Steven E Brenner

Tim J P Hubbard

Cyrus Chothia

Alexey G Murzin

Affiliations

Soon will be listed here.

Abstract

The SCOP (Structural Classification of Proteins) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are grouped into species and hierarchically classified into families, superfamilies, folds and classes. Recently, we introduced a new set of features with the aim of standardizing access to the database, and providing a solid basis to manage the increasing number of experimental structures expected from structural genomics projects. These features include: a new set of identifiers, which uniquely identify each entry in the hierarchy; a compact representation of protein domain classification; a new set of parseable files, which fully describe all domains in SCOP and the hierarchy itself. These new features are reflected in the ASTRAL compendium. The SCOP search engine has also been updated, and a set of links to external resources added at the level of domain entries. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.

Citing Articles

Genome sequencing and de novo and reference-based genome assemblies of Bos indicus breeds.

Chakraborty A, Bisht M, Saxena R, Mahajan S, Pulikkan J, Sharma V Genes Genomics. 2023; 45(11):1399-1408.

PMID: 37231295 DOI: 10.1007/s13258-023-01401-w.

SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning.

Chandonia J, Guan L, Lin S, Yu C, Fox N, Brenner S Nucleic Acids Res. 2021; 50(D1):D553-D559.

PMID: 34850923 PMC: 8728185. DOI: 10.1093/nar/gkab1054.

SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database.

Chandonia J, Fox N, Brenner S Nucleic Acids Res. 2018; 47(D1):D475-D481.

PMID: 30500919 PMC: 6323910. DOI: 10.1093/nar/gky1134.

Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study.

Weissenborn S, Walther D Front Plant Sci. 2017; 8:1831.

PMID: 29163570 PMC: 5664361. DOI: 10.3389/fpls.2017.01831.

From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns.

Salentin S, Adasme M, Heinrich J, Haupt V, Daminelli S, Zhang Y Sci Rep. 2017; 7(1):11401.

PMID: 28900272 PMC: 5595859. DOI: 10.1038/s41598-017-11924-4.

References

van den Ent F, Lockhart A, Kendrick-Jones J, Lowe J . Crystal structure of the N-terminal domain of MukB: a protein involved in chromosome partitioning. Structure. 1999; 7(10):1181-7. DOI: 10.1016/s0969-2126(00)80052-0. View

Karplus K, Barrett C, Hughey R . Hidden Markov models for detecting remote protein homologies. Bioinformatics. 1999; 14(10):846-56. DOI: 10.1093/bioinformatics/14.10.846. View

FITCH W . Homology a personal view on some of the problems. Trends Genet. 2000; 16(5):227-31. DOI: 10.1016/s0168-9525(00)02005-9. View

Hopfner K, Karcher A, Shin D, Craig L, Arthur L, Carney J . Structural biology of Rad50 ATPase: ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily. Cell. 2000; 101(7):789-800. DOI: 10.1016/s0092-8674(00)80890-9. View

Lerman J, Robblee J, Fairman R, Hughson F . Structural analysis of the neuronal SNARE protein syntaxin-1A. Biochemistry. 2000; 39(29):8470-9. DOI: 10.1021/bi0003994. View

Lowe J, Cordell S, van den Ent F . Crystal structure of the SMC head domain: an ABC ATPase with 900 residues antiparallel coiled-coil inserted. J Mol Biol. 2001; 306(1):25-35. DOI: 10.1006/jmbi.2000.4379. View

Qian J, Stenger B, Wilson C, Lin J, Jansen R, Teichmann S . PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Nucleic Acids Res. 2001; 29(8):1750-64. PMC: 31319. DOI: 10.1093/nar/29.8.1750. View

Brenner S . A tour of structural genomics. Nat Rev Genet. 2001; 2(10):801-9. DOI: 10.1038/35093574. View

Gough J, Karplus K, Hughey R, Chothia C . Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 2001; 313(4):903-19. DOI: 10.1006/jmbi.2001.5080. View

10.

Westbrook J, Feng Z, Jain S, Bhat T, Thanki N, Ravichandran V . The Protein Data Bank: unifying the archive. Nucleic Acids Res. 2001; 30(1):245-8. PMC: 99110. DOI: 10.1093/nar/30.1.245. View

11.

Chandonia J, Walker N, Lo Conte L, Koehl P, Levitt M, Brenner S . ASTRAL compendium enhancements. Nucleic Acids Res. 2001; 30(1):260-3. PMC: 99063. DOI: 10.1093/nar/30.1.260. View

12.

Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy S . The Pfam protein families database. Nucleic Acids Res. 2001; 30(1):276-80. PMC: 99071. DOI: 10.1093/nar/30.1.276. View

13.

Bernstein F, Koetzle T, Williams G, Meyer Jr E, Brice M, Rodgers J . The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977; 112(3):535-42. DOI: 10.1016/s0022-2836(77)80200-3. View

14.

Murzin A, Brenner S, Hubbard T, Chothia C . SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995; 247(4):536-40. DOI: 10.1006/jmbi.1995.0159. View

15.

Brenner S, Chothia C, Hubbard T, Murzin A . Understanding protein structure: using scop for fold interpretation. Methods Enzymol. 1996; 266:635-43. DOI: 10.1016/s0076-6879(96)66039-x. View

16.

Fernandez I, Ubach J, Dulubova I, Zhang X, Sudhof T, Rizo J . Three-dimensional structure of an evolutionarily conserved N-terminal domain of syntaxin 1A. Cell. 1998; 94(6):841-9. DOI: 10.1016/s0092-8674(00)81742-0. View

17.

Brenner S, Barken D, Levitt M . The PRESAGE database for structural genomics. Nucleic Acids Res. 1998; 27(1):251-3. PMC: 148148. DOI: 10.1093/nar/27.1.251. View

18.

Misura K, Scheller R, Weis W . Three-dimensional structure of the neuronal-Sec1-syntaxin 1a complex. Nature. 2000; 404(6776):355-62. DOI: 10.1038/35006120. View