SCOP_structural_classification_of_Protei.ppt
- 2. A Structural Classification of Proteins Database for the Investigation of Sequences and Structures Website: http://scop.mrc-lmb.cam.ac.uk/scop/ Manual classification of protein structural domains based on similarities of their structures and amino acid sequences. Created in 1994. Maintained by Alexei G. Murzin and his colleagues at the Laboratory of Molecular Biology in Cambridge, England.
- 3. • It provides a detailed and comprehensive description of the relationships of known Protein structures. • Classification is on hierarchical levels. • It is freely accessible. • Current version of SCOP is 2.03 (October 2013)- http://scop.berkeley.edu/
- 4. Family (identical structure and function) ◦ All proteins that have residue identities of 30% and greater or Pairwise sequence similarity > 25% ◦ The proteins that have lower sequence identities but whose functions and structures are very similar. ◦ Clear evolutionary relationship Superfamily (common structure and function) ◦ Probable common ancestry ◦ Families whose proteins have low sequence identities but whose structures and, in many cases, functional features suggest that a common evolutionary origin is probable. ◦ variable and constant domains of immunoglobulin.
- 5. Fold (common core structure ) ◦ Major structural similarity ◦ SSE’s in similar arrangement ◦ Superfamilies and families are defined as having a common fold if their proteins have the same major secondary structures in the same arrangement and with the same topological connections. Class ◦ Similar secondary structure content ◦ Folds have been grouped into five structural classes: 1. all-α, those whose structure is essentially formed by α- helices; 2. all-β, those whose structure is essentially formed by β- sheets; 3. α/β, those with α-helices and β-strands; 4. α+β, those in which α-helices and β-strands are largely segregated; 5. multi-domain, those with domains of different fold and for which no homologues are known at present.
- 7. Alternating Parallel sheets Anti-parallel β sheets
- 8. FOLD
- 10. Access methods: ◦ Enter SCOP at the top of the hierarchy ◦ Keyword search of SCOP entries ◦ From a PDB identifier ◦ SCOP parseable files (MRC site) ◦ All SCOP releases and reclassified entry history (MRC site) ◦ pre-SCOP - preview of the next release ◦ SCOP domain sequences and pdb-style coordinate files (ASTRAL) ◦ Hidden Markov Model library for SCOP superfamilies (SUPERFAMILY) ◦ Structural alignments for proteins with non-trivial relationships (SISYPHUS) ◦ Online resources of potential interest to SCOP users
- 11. top of the hierarchy
- 13. Protein Structure Classification - SCOP
- 14. Protein Structure Classification - SCOP
- 15. Protein Structure Classification - SCOP
- 16. Protein Structure Classification - SCOP
- 18. SCOP classification is used: 1. As reference set of data to develop automatic classification methods used in analyzing families, superfamilies, and folds 2. For integrative structural data mining to develop predictive methods and structure-comparison tools
- 19. Understanding evolution of protein enzymatic functions, evolutionary change of protein folds, hierarchical structural evolution. To study distantly related proteins with the same fold. To study sequence and structure variability and its dependence in homologous proteins To derive amino acid similarity matrices and substitution tables useful for sequence comparison and fold recognition studies
- 20. To study the structural anatomy of folds and domains, to extract structural principles for use in protein design experiments SCOP domains have been used to study combinations of different domains and their decomposition in multidomain proteins Recent structural genome projects have been using SCOP extensively in identifying new targets SCOP families have been used for developing value-added and more specialized databases
- 21. Experimental structural biologists: to explore the region of structure space near their protein of current research. Molecular biologists: the categorization assists in locating proteins of interest and the links make exploration easy. Theoreticians will likely find it most useful to browse the wide range of protein folds currently known. SCOP will find pedagogical use, for it organizes structures in an easily comprehensible manner
- 22. SCOP can be used for detailed searching of particular families. Analysis of the growth of structural data: gives an estimate of the total numbers of protein folds and superfamilies that exist in nature. It provides a level of classification not present in the Protein Data Bank (PDB).