The FSSP File

  • The FSSP file is an output from the DALI program.
  • For every PDB file submitted to the ProKnow program, at least one FSSP file is needed.
  • If the PDB file has multiple domains, FSSP file for each domain need to be submitted.
  • Please submit your PDB file to the DALI Server and use the files obtained (the FSSP files) for input into the ProKnow program.

    • An example FSSP file

    FSSP      FAMILIES OF STRUCTURALLY SIMILAR PROTEINS, VERSION 1.1 (Apr 1 1998)
CREATED   Mon Oct 29 20:31:27 GMT 2001 for dali on jura
METHOD    Dali ver. 2.0: Holm, L., Sander, C. (1993) J.Mol.Biol. 233,123-138
DATABASE  2860 protein chains
PDBID     1a0aA
HEADER    COMPLEX (TRANSCRIPTION FACTOR/DNA)
COMPND    phosphate system positive regulatory protein pho4 fragment (bhlh) biological_unit DNA fragment (uasp2(17))
SOURCE    (saccharomyces cerevisiae) baker's yeast
AUTHOR    T.Shimizu A.Toumoto K.Ihara M.Shimizu Y.Kyogoku N.Ogawa Y.Oshima T.Hakoshima
SEQLENGTH    63
NALIGN       10
WARNING   pairs with Z<2.0 are structurally dissimilar

## SUMMARY: PDB/chain identifiers and structural alignment statistics
NR. STRID1 STRID2  Z   RMSD LALI LSEQ2 %IDE REVERS PERMUT NFRAG TOPO PROTEIN
 1: 1a0aA  1a0aA  11.6  0.0   63    63  100      0      0     1 S    phosphate system positive regulatory protein pho4 fragm
 2: 1a0aA  1a0aB   5.1  2.4   60    63   82      0      0     4 S    phosphate system positive regulatory protein pho4 fragm
 3: 1a0aA  1am9A   3.6  2.5   53    80   25      0      0     4 S    sterol regulatory element binding protein 1a fragment (
 4: 1a0aA  1an2A   3.4  2.4   54    86   25      0      0     4 S    max protein fragment (myn protein) biological_unit DNA
 5: 1a0aA  1mdyA   2.9  3.2   51    68   14      0      0     5 S    Myod basic-helix-loop-helix (bhlh) domain (residues 102
 6: 1a0aA  2xat    2.9  2.1   38   208    3      0      0     5 S    xenobiotic acetyltransferase biological_unit
 7: 1a0aA  3pviA   2.5  4.3   48   156    7      0      0     4 S    pvuii endonuclease Mutant DNA (5'-d(TpGpApCpCpApGpCpTpG
 8: 1a0aA  1fgjA   2.3  4.0   55   499    0      0      0     5 S    hydroxylamine oxidoreductase
 9: 1a0aA  1an4A   2.2  4.7   52    65   20      0      0     4 S    usf fragment (upstream stimulatory factor 1) Mutant bio
10: 1a0aA  1qgrA   2.1  3.8   44   871    3      0      0     3 S    importin beta subunit (karyopherin beta-1, nuclear fact