scholarly journals The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures

2019 ◽  
Vol 48 (D1) ◽  
pp. D376-D382 ◽  
Author(s):  
Antonina Andreeva ◽  
Eugene Kulesha ◽  
Julian Gough ◽  
Alexey G Murzin
Keyword(s):  
Protein Structures ◽  
Structural Data ◽  
Web Interface ◽  
Structural Classification ◽  
Scop Database ◽  
Structural Relationships ◽  
Almost All ◽  
Structural Classification Of Proteins ◽  
Representative Family

Abstract The Structural Classification of Proteins (SCOP) database is a classification of protein domains organised according to their evolutionary and structural relationships. We report a major effort to increase the coverage of structural data, aiming to provide classification of almost all domain superfamilies with representatives in the PDB. We have also improved the database schema, provided a new API and modernised the web interface. This is by far the most significant update in coverage since SCOP 1.75 and builds on the advances in schema from the SCOP 2 prototype. The database is accessible from http://scop.mrc-lmb.cam.ac.uk.

scholarly journals SCOP, Structural Classification of Proteins Database: Applications to Evaluation of the Effectiveness of Sequence Alignment Methods and Statistics of Protein Structural Data

1998 ◽  
Vol 54 (6) ◽  
pp. 1147-1154 ◽  
Author(s):  
Tim J. P. Hubbard ◽  
Bart Ailey ◽  
Steven E. Brenner ◽  
Alexey G. Murzin ◽  
Cyrus Chothia
Keyword(s):  
Protein Structures ◽  
Structural Data ◽  
Evolutionary Relationships ◽  
Structural Classification ◽  
Comprehensive Description ◽  
Database Applications ◽  
The Third ◽  
Sequence Search ◽  
Structural Classification Of Proteins

The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known protein structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures. The database and its associated files are freely accessible from a number of WWW sites mirrored from URL http://scop.mrc-lmb.cam.ac.uk/scop/.

scholarly journals SCOP: a Structural Classification of Proteins database

1999 ◽  
Vol 27 (1) ◽  
pp. 254-256 ◽  
Author(s):  
T. J. P. Hubbard ◽  
B. Ailey ◽  
S. E. Brenner ◽  
A. G. Murzin ◽  
C. Chothia
Keyword(s):  
Structural Classification ◽  
Structural Classification Of Proteins

scholarly journals Molecular mechanisms of fat deposition: <i>IL-6</i> is a hub gene in fat lipolysis, comparing thin-tailed with fat-tailed sheep breeds

2021 ◽  
Vol 64 (1) ◽  
pp. 53-68
Author(s):  
Sana Farhadi ◽  
Jalil Shodja Ghias ◽  
Karim Hasanpur ◽  
Seyed Abolghasem Mohammadi ◽  
Esmaeil Ebrahimie
Keyword(s):  
Fatty Acid ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Structural Classification ◽  
Hub Genes ◽  
Sheep Breeds ◽  
Ppi Networks ◽  
Structural Classification Of Proteins

Abstract. Tail fat content affects meat quality and varies significantly among different breeds of sheep. Ghezel (fat-tailed) and Zel (thin-tailed) are two important Iranian local sheep breeds with different patterns of fat storage. The current study presents the transcriptome characterization of tail fat using RNA sequencing in order to get a better comprehension of the molecular mechanism of lipid storage in the two mentioned sheep breeds. Seven (Zel = 4 and Ghezel = 3) 7-month-old male lambs were used for this experiment. The results of sequencing were analyzed with bioinformatics methods, including differentially expressed genes (DEGs) identification, functional enrichment analysis, structural classification of proteins, protein–protein interaction (PPI) and network and module analyses. Some of the DEGs, such as LIPG, SAA1, SOCS3, HIF-1α, and especially IL-6, had a close association with lipid metabolism. Furthermore, functional enrichment analysis revealed pathways associated with fat deposition, including “fatty acid metabolism”, “fatty acid biosynthesis” and “HIF-1 signaling pathway”. The structural classification of proteins showed that major down-regulated DEGs in the Zel (thin-tailed) breed were classified under transporter class and that most of them belonged to the solute carrier transporter (SLC) families. In addition, DEGs under the transcription factor class with an important role in lipolysis were up-regulated in the Zel (thin-tailed) breed. Also, network analysis revealed that IL-6 and JUNB were hub genes for up-regulated PPI networks, and HMGCS1, VPS35 and VPS26A were hub genes for down-regulated PPI networks. Among the up-regulated DEGs, the IL-6 gene seems to play an important role in lipolysis of tail fat in thin-tailed sheep breeds via various pathways such as tumor necrosis factor (TNF) signaling and mitogen-activated protein kinase (MAPK) signaling pathways. Due to the probable role of the IL-6 gene in fat lipolysis and also due to the strong interaction of IL-6 with the other up-regulated DEGs, it seems that IL-6 accelerates the degradation of lipids in tail fat cells.

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