FSSP database

Holm L and C Sander 1994. The FSSP Database of Structurally Aligned Protein Fold Families. Ni Acids Research 22 3600-3609. 

Holm, L. and Sander, C. (1996) The FSSP database fold classification based on structure-structure alignment of proteins. Nucleic Acids Res. 24, 206-209. 

Holm, L., and Sander, C. (1994). The FSSP database of structurally-aligned protein fold families. Nucl. Acids Res. 22, 3600-3609. 

FSSP is the database that compares all PDB structures using the DaU program and processes them into domains. FSSP data can be accessed at http //www.bioinfo.biocenter. helsinki.fi 8080/dali/ by either searching for a PDB structure of interest or submitting the coordinates of a new structure and requesting DALI to perform a custom search against the FSSP database. 

CATH, FSSP Sequence-structure classification databases... 

The SCOP database is curated manually, with the objective of placing proteins in the correct evolutionary framework based on conserved structural features. Two similar enterprises, the CATH (class, architecture, topology, and homologous superfamily) and FSSP (/old classification based on structure-structure alignment of proteins) databases, make use of more automated methods and can provide additional information. 

The EMBL in Heidelberg provides a multitude of services that can be hclprful Ah the molecular modeler. DSSF, HSSFt FSSP, FDBFINDER, PDBREPORT, and PDB SELECT are derived protein databases. They are based on data from the Protein Data Bank of 3D structures and the Swissprot database of LD protein sequences. The data and related software can be obtained vis anonymous FTP or, mote easily these days, via the WWW. 

As mentioned above, several of these approaches have been employed to generate exhaustive clusterings of the protein structures into structural classes available via the resulting databases (DDD/FSSP/Dali [102], 3Dee [79], JOY/HOMSTRAD/DDBASE [112-114], structure cores LPFC [115]), These superposition-based classifications are complemented with classi-... 

If the structure you are considering is already in the PDB, then these similarities can be found in a number of databases including SCOP [48] (http //scop.mrc-lmb. cam.ac.uk/scop/index.html), CATH [49] (http //www.biochem.ucl.ac.uk/bsm/cath/ cath.html), and FSSP/Dali [50] (http //ekhidna.biocenter.helsinki.fi/dali/). However, if the structure is not yet in the PDB, you will need to perform your own structure search to compare your structure to all other known structures. In a broad sense, structure searching is similar to sequence searches however, the methods used are very different and quite a bit slower. Some standard methods are Dali [51] (http //ekhidna.biocenter.helsinki.fi/dali/), VAST [52] (http //www.ncbi.nhn.nih.gov/ Structure/VAST/vastsearch.html), and SSM [53] (http //www.ebi.ac.uk/msd/Services. html). 

Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C., 1995. SCOP A structural classification of proteins database for the investigation of sequences and structures./. Mol. Biol 247 536-540. Hadley, C., and Jones, D. T., 1999. A systematic comparison of protein structure classification SCOP, CATH and FSSP. Structure Fold. Des. 7 1099-1112. 

Links. PDB s search engine, the Structme Explorer, can be used to retrieve PDB records, as shown in Figure 5.2. The Structure Explorer is also the primary database of links to third-party aimotation of PDB structure data. There are a number of links maintained in the Structure Explorer to Internet-based three-dimensional structure services on other Web sites. Figme 5.2 shows the Structure Summary for the protein bamase (IBNR Bycroft et al., 1991). The Structure Explorer also provides links to special project databases maintained by researchers interested in related topics, such as structural evolution (FSSP Holm and Sander, 1993), structure-structure similarity (DALI Holm and Sander, 1996), and protein motions (Gerstein et al., 1994). Links to visualization tool-ready versions of the structure are provided, as well as authored two-dimensional images that can be very helpful to see how to orient a three-dimensional structure for best viewing of certain features such as binding sites. 

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