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Research Paper | Computer Science | India | Volume 2 Issue 10, October 2013 | Popularity: 6.9 / 10

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The FSSP database: Fold Classification based on Structure Structure alignment of Proteins

Manish Kumar, Kapil Govil

Abstract: FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB) (1). The current release has 2860 entries. The FSSP (http: //srs. ebi. ac. uk/srsbin/cgi-bin/wgetz-page+LibInfo+-id+5Ti2u1RffMj+-lib+FSSP) database presently contains an extended structural family for every of 330 representative protein chains. Each information set contains structural alignments of one search structure with all different structurally significantly similar proteins within the representative set, for remote homologs, below 30 % sequence identity, Further as all structures within the Protein Data Bank with 70-30 % sequence identity relative to the search structure (medium homologs). For Very close homologs, which are above 70 % sequence identity, they are excluded as they rarely have marked structural variations. The alignments of remote homologs are the result of pair wise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based strictly on the 3D co-ordinates of the proteins and are derived by automatic (objective) structure comparison programs. The importance of structural similarity is estimated based on statistical criteria. The FSSP info is obtainable electronically from the EMBL file server and by anonymous ftp (file transfer protocol).

Keywords: PDB, FSSP, DALI, families, Z-score

Edition: Volume 2 Issue 10, October 2013

Pages: 23 - 25

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