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David Koes added FXIa_The_best_SMARTS_expression__.tex
over 8 years ago
Commit id: 875079a72cdc4f630b2a32a203c3989846a9ac44
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FXIa
The best SMARTS expression and approach for FXIa performed significantly better than random performance for the FOMS, but not the VAMS method (cite table). Inhibition of FXIa relies on hydrogen-bonding with many residues. Only one of the pockets and its interaction with a His57 by hydrogen bonding and a stacking interaction are covered by our SMARTS expression and fragment pre-alignment (cite FXIa). There are many other hydrogen-bond interactions that include hydrogen bonding with Asp189, Gly216, and Gly218 backbones that are not covered by our SMARTS expression and fragment pre-alignment. Similar to most other protein targets in the MUV dataset, FOMS would not fully capture the complete binding mode of compounds screened, which most likely led to its poor performance (cite table).
Docking of 2FDA with active compounds from the MUV dataset revealed 5 hydrophobic pockets, with only one being covered by our fragment pre-alignment. Many hydrogen-bonding interactions were revealed, including His57 and the inhibitor. Because our best SMARTS expression and fragment pre-alignment only covered the interaction with His57 and 1 of 5 potential pockets to be filled, it makes sense that FOMS did not yield high performance.
More specific SMARTS expressions led to higher performance for VAMS, whereas the least specific SMARTS expression led to highest performance for FOMS (cite table). (explanation for both?)
