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David Koes added FAK_FAK_with_its_best__.tex
over 8 years ago
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FAK
FAK with its best SMARTS expression and approach performed significantly better than random performance for the FOMS method (cite stat table). Even with the best SMARTS expression and approach, the VAMS method performed worse than random performance for FAK (cite table).
FAK inhibition relies on hydrogen-bonding interactions with Cys502 and Arg426, along with an important hydrophobic interaction with Leu553 in the active site (cite FAK). Only the interaction with Cys502 is covered by the SMARTS expression and fragment pre-alignment. This indicates that other decoy compounds could be scored more favorably with FOMS since it would only focus on the fragment choice that highlights one of 3 key interactions. FAK inhibitors are supposed to be ATP-competitive, so it makes sense that only a small piece of the inhibitor cannot represent the entire binding mode of inhibition.
When docking with smina was performed on 3BZ3 and the active compounds that were covered by our SMARTS expressions, there were 5 pockets possible for filling observed, with only one covered by our fragment pre-alignment. In addition, hydrogen-bonding with Cys502 and Arg426 were observed frequently between active conformers. Our fragment pre-alignment and SMARTS expression would only cover the interaction with Cys502. Because there are more than one interaction and many pockets to be filled, it makes sense that FOMS was not able to yield high performance.
More specific SMARTS expressions led to higher performance for both methods (cite table). This makes sense as the best SMARTS expression and fragment pre-alignment covered the hydrogen-bonding interaction with Cys502, vital for FAK inhibition.
