From Proteinfunction.net

The basic assumption of the method is that proteins with similar structure might have similar function. Protein function is strongly related with its structure since protein functions by interacting with other proteins or chemicals and structure limits the possibility of its interaction modes. Moreover, structure similarity could fill the gap that is overlooked with sequence based method which can only detect close sequence similarity since structural similarity could be detectable from low sequence similar proteins. Accordingly, the basic method to infer function using structure information is comparion of overall three-dimentional structures.
Like BLAST , we can search similar protein structures via various web-servers and tools. Recently basic structure comparison and clustering method are combined for more accurate function prediction (e. g. PDB-UF, ELISA )

 

Contents 1 Structure comparison tool 2 Database of Protein Structure Classification 2.1 SCOP 2.2 CATH

Structure comparison tool

• DALI

• CE

• VAST

• 3D-Hit
  

• SHEBA/LSHEBA

Database of Protein Structure Classification

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  SCOP

  
  Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
• [edit]

  CATH

  
  The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank (PDB, Berman et al. 2003). Only crystal structures solved to resolution better than 4.0 angstroms are considered, together with NMR structures. All non-proteins, models, and structures with greater than 30% "C-alpha only" are excluded from CATH. This filtering of the PDB is performed using the SIFT protocol (Michie et al., 1996). Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy: Class, Architecture, Topology (fold family) and Homologous superfamily (Orengo et al., 1997).