David Koes edited Results.tex  over 8 years ago

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\subsection*{Rho-Kinase2}  Virtual screening results Rho-Kinase2 are shown in Figure~\ref{rho} and are similar to those of PKA. FOMS achieves an AUC of 0.94, VAMS an AUC of 0.56, and RDKit and AUC of 0.34. The best shape constraints match or exceed the performance of FOMS.  The best SMARTS expression and approach for Rho-Kinase2 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 Rho-Kinase2 (cite stats table).   Similar to PKA, Rho-Kinase2 inhibitors are relatively small compared to other inhibtors and have few electrostatic interactions. In the case of 2H9V and its inhibitor, there are three hydrogen-bonding interactions with conserved Met, Asn, and Asp. There are also important hydrophobic interactions with other residues inside the pocket (cite Rho). Our SMARTS expression and fragment pre-alignment covers the hydrogen-bonding interaction with the Met and important hydrophobic interactions with conserved Val and Leu residues. This most likely led to the high performance of FOMS for Rho-Kinase2 (cite table).  % The best SMARTS expression and approach for Rho-Kinase2 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 Rho-Kinase2 (cite stats table).   %Similar to PKA, Rho-Kinase2 inhibitors are relatively small compared to other inhibtors and have few electrostatic interactions. In the case of 2H9V and its inhibitor, there are three hydrogen-bonding interactions with conserved Met, Asn, and Asp. There are also important hydrophobic interactions with other residues inside the pocket (cite Rho). Our SMARTS expression and fragment pre-alignment covers the hydrogen-bonding interaction with the Met and important hydrophobic interactions with conserved Val and Leu residues. This most likely led to the high performance of FOMS for Rho-Kinase2 (cite table).  %  More specific SMARTS expressions led to lower performance for both the FOMS and VAMS methods. (explanation for why this is ).