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David Koes added PKA_The_best_SMARTS_expression__.tex
over 8 years ago
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PKA
The best SMARTS expression and approach for PKA performed significantly better than random performance for both FOMS and VAMS (cite stats table). The FOMS approach was significantly better than the VAMS approach for PKA (cite stats table).
Like many other targets in this dataset, PKA inhibitors interact with the ATP binding site. These inhibitors are relatively smaller in size compared to other inhibitors and have few electrostatic interactions. In the example of 1Q8U and its inhibitor, there is only one hydrogen bond with Val123, where the rest of the ligand makes multiple Van der Waals contacts with other parts of the target (cite PKA). SMARTS expressions and fragment pre-alignment covers the only electrostatic interaction and most of the hydrophobic interactions involved in PKA inhibitors, which most likely led to the high performance of FOMS (cite table).
More specific SMARTS expressions led to higher performance for FOMS (cite table). This makes sense as the more specific fragment choice would cover the only necessary hydrogen-bond interaction with the receptor. Less specific SMARTS expressions led to higher performance for the VAMS method (cite table). (explanation for why this is).
