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Figure 2
Validation results for LigSearch runs on 200 randomly selected enzymes with no three-dimensional structural model in the PDB. (a) Histogram of the molecular-similarity scores for the closest PDB ligand match, as computed by the SMSD program, to any of the enzyme's cognate ligands. (b) Histogram of the sequence identities between the query enzyme sequence and the PDB protein from which the best ligand match has a similarity of 0.8 or greater to one of the cognate ligands. (c) Histogram of the LigSearch scores for the best matches to cognate ligands. The counts are grouped into four sets according to the similarity score, s, of the best-matching molecule. Lowest similarity scores (s < 0.7) are shown in blue, scores 0.7 ≤ s < 0.8 are shown in green, scores 0.8 ≤ s < 0.9 are shown in orange and closest matches with s ≥ 0.9 are shown in red. (d) Histogram of counts of molecules with similarity s ≥ 0.8 to at least one of the enzyme's cognate ligands as returned by LigSearch for the non-PDB hits. The cognate molecules themselves are, of course, excluded from the results.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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