Prediction of calcium-binding sites by combining loop-modeling with machine learning

BMC Structural Biology

Table 3 Ten FEATURE predictions confirmed by direct experimental evidence.

Two predictions of which calcium binding have been observed experimentally near the predicted sites. Column 2 lists protein name that is PDB code followed by the chain identifier. We build structures for gaps of which 3D structures are not presented in the original PDB files. Information of these structures, referred as "loop", is given in column 3-5. Column 6 lists the distances between the predicted sites and the experimentally observed sites (SiteDis). Column 7 and 8 list FEATURE scores at the predicted sites in the structures where loop structures are missing (Gap) and the structures of which loop structures were rebuilt by modeling methods (Loop). These two are holo structures, but their calcium-binding sites are not completely structured. FEATURE is able to identify these sites in the presence of the rebuilt loop structures.

ISSN: 1472-6807