{"id":150,"date":"2014-04-18T22:08:57","date_gmt":"2014-04-18T22:08:57","guid":{"rendered":"http:\/\/pbwww.che.sbg.ac.at\/wordpress\/?page_id=150"},"modified":"2021-02-13T17:30:14","modified_gmt":"2021-02-13T16:30:14","slug":"sisy-pairwise","status":"publish","type":"page","link":"https:\/\/pbwww.services.came.sbg.ac.at\/?page_id=150","title":{"rendered":"SISY pairwise"},"content":{"rendered":"

The SISY pairwise set contains protein pairs selected from all three SISYPHUS categories Homologous<\/i><\/a>, Fold<\/i><\/a>, Fragment<\/i><\/a> [3]<\/a>. In general, the difficulty for a comparison method increases from homology to fragment [1]<\/a>. Note that the SISYPHUS database contains multi-chain domains, which means that a molecule in the alignment may consist of more than one peptide chain.<\/p>\n

To extract the most difficult case from a family (not more than one per family) we applied the following strategy for each family:<\/p>\n

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  • Check all possible pairs for a permutation and take the one with the lowest sequence similarity. Assign class P<\/b><\/span>. Done with this family and proceed to the next one.<\/li>\n
  • Superimpose all pairs according to the SISYPHUS alignment. If there are one or more pairs with rmsd > 4A, take the one with the largest rmsd. Assign class C<\/b><\/span>. Done with this family and proceed to the next one.<\/li>\n
  • A so called SISYPHUS construct contains for each structure all the residues between the first aligned residue pair and the last aligned residue pair. If the larger construct is more then twice a long as the smaller one take it. If there are multiple pairs above the cutoff, take the one with the largest size difference. Assign class I<\/b><\/span>. Done with this family and proceed to the next one.<\/li>\n
  • Run a Smith-Waterman sequence alignment for all pairs. If there is a pair with less than 40% sequence identity, take it. If there are multiple pairs below the cutoff, take the one with the lowest sequence identity. Done with this family and proceed to the next one.<\/li>\n
  • If none of these rules applies no pair is selected for this family.<\/li>\n<\/menu>\n

    The corresponding PDB files contain only the chain(s) used in the alignment. The table can be sorted alphabetically or numerically by a mouse click in the column header.<\/p>\n