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David Koes added subsubsection_Cathepsin_G_Cathepsin_G__.tex
over 8 years ago
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\subsubsection*{Cathepsin G}
Cathepsin G with its best approach and SMARTS expression, FOMS performed significantly better than random performance (cite stats table). For VAMS however, Cathepsin G with its best approach and SMARTS expression performed slightly worse than random chance (cite table). This indicates that for Cathepsin G, FOMS was a better performing screening method.
According to the study on the crystal structure of Cathepsin G with its inhibitor, Cathepsin G has 4 hydrophobic pockets that can be optimized for binding, each potentially being filled by a napthol group. Both FOMS and VAMS were pre-aligned to the deepest pocket in the active site, S1, the region that contributes the most to stabilizing the crystal structure (cite cathg). Although this is the most important interaction for a Cathepsin G inhibitor, filling the other pocket located at S3/S4 as referenced can contribute as much as 50 fold for increasing stability (cite cathg).
Docking of 1T32 with its active set from MUV using smina revealed 4 main pockets that were filled, the same shown in the previous study. The S1 pocket was filled the most frequently, with S3/S4 being filled second-most. This indicates that we pre-aligned our fragment to the most important pocket, however the S3/S4 pocket is also vital for Cathepsin G inhibition.
In general, less specific SMARTS expressions performed better for Cathepsin G for both FOMS and VAMS. (explanation for that).
