 | |
| Content | |
|---|---|
| Description | Protein Structure Classification |
| Contact | |
| Research center | Laboratory of Molecular Biology |
| Authors | Alexey G. Murzin, Steven E. Brenner, Tim J. P. Hubbard, and Cyrus Chothia |
| Primary citation | PMID 7723011 |
| Release date | 1994 |
| Access | |
| Website | http://scop.mrc-lmb.cam.ac.uk/scop/ |
| Miscellaneous | |
| Version | 1.75 (June 2009; 110,800 domains in 38,221 structures classed as 3,902 families)[1] |
| Curation policy | manual |
| Content | |
|---|---|
| Description | SCOP - extended |
| Contact | |
| Authors | Naomi K. Fox, Steven E. Brenner, and John-Marc Chandonia |
| Primary citation | PMID 24304899 |
| Access | |
| Website | https://scop.berkeley.edu |
| Miscellaneous | |
| Version | 2.07 (March 2018; 276,231 domains in 87,224 structures classed as 4,919 families)[2] |
| Curation policy | manual (new classifications) and automated (new structures, BLAST) |
The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different superfamilies, and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in "families", and are assumed to have a closer common ancestor.
Similar to CATH and Pfam databases, SCOP provides a classification of individual structural domains of proteins, rather than a classification of the entire proteins which may include a significant number of different domains.
The SCOP database is freely accessible on the internet. SCOP was created in 1994 in the Centre for Protein Engineering and the Laboratory of Molecular Biology.[3] It was maintained by Alexey G. Murzin and his colleagues in the Centre for Protein Engineering until its closure in 2010 and subsequently at the Laboratory of Molecular Biology in Cambridge, England.[4][5][6][1]
The work on SCOP 1.75 has been discontinued in 2014. Since then SCOPe team from UC Berkeley has been responsible for updating the database in a compatible manner, with a combination of automated and manual methods. As of April 2019[update], the latest release is SCOPe 2.07 (March 2018).[2]
The new Structural Classification of Proteins version 2 (SCOP2) database was released at the beginning of 2020. The new update featured an improved database schema, a new API and modernised web interface. This was the most significant update by the Cambridge group since SCOP 1.75 and builds on the advances in schema from the SCOP 2 prototype.[7]
- ^ a b Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (January 2008). "Data growth and its impact on the SCOP database: new developments". Nucleic Acids Research. 36 (Database issue): D419-25. doi:10.1093/nar/gkm993. PMC 2238974. PMID 18000004.
- ^ a b Chandonia JM, Fox NK, Brenner SE (January 2019). "SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database". Nucleic Acids Research. 47 (D1): D475–D481. doi:10.1093/nar/gky1134. PMC 6323910. PMID 30500919.
- ^ Murzin AG, Brenner SE, Hubbard T, Chothia C (April 1995). "SCOP: a structural classification of proteins database for the investigation of sequences and structures". Journal of Molecular Biology. 247 (4): 536–40. doi:10.1016/S0022-2836(05)80134-2. PMID 7723011.
- ^ Hubbard TJ, Ailey B, Brenner SE, Murzin AG, Chothia C (January 1999). "SCOP: a Structural Classification of Proteins database". Nucleic Acids Research. 27 (1): 254–6. doi:10.1093/nar/27.1.254. PMC 148149. PMID 9847194.
- ^ Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C (January 2000). "SCOP: a structural classification of proteins database". Nucleic Acids Research. 28 (1): 257–9. doi:10.1093/nar/28.1.257. PMC 102479. PMID 10592240.
- ^ Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG (January 2004). "SCOP database in 2004: refinements integrate structure and sequence family data". Nucleic Acids Research. 32 (Database issue): D226-9. doi:10.1093/nar/gkh039. PMC 308773. PMID 14681400.
- ^ Andreeva A, Kulesha E, Gough J, Murzin AG (January 2020). "SCOP database in 2020: : expanded classification of representative family and superfamily domains of known protein structures". Nucleic Acids Research. 48 (Database issue): D376–D382. doi:10.1093/nar/gkz1064. PMC 7139981. PMID 31724711.