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David Koes edited Results.tex
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\section{Results}
General Observations:
Protein targets with ligands that have many key interactions for their binding mode did not perform as favorably as targets with ligands that have a few key interactions. Targets with relatively few interactions may have the important features for protein inhibition covered by the SMARTS expression and fragment pre-alignment. These targets may easily reject compounds that did not match the SMARTS expression key for understanding the mode of inhibition.
In general, FOMS performed better than VAMS for every protein target. This indicates that it is an effective pre-screen, when considering the earlier success of VAMS (cite VAMS). In general, more specific SMARTS expressions led to a higher performance for both FOMS and VAMS. Higher specificity of fragment choice will lead to identifying singly the most important interactions involved in the binding mode of the ligand. In general, the interaction point method for both FOMS and VAMS yielded the highest performance (cite table). The interaction point method is able to include specific areas where interactions are likely to occur between the receptor and ligand. Logically, this approach should yield the highest performance since it uses the most information involved in ligand-receptor interactions.
Fragment Selection:
The literature that cites the crystal structure from PDB should be conferred for fragment choice when determining the SMARTS expression for each protein target. Information about the important residues in the protein and which pocket(s)/interactions are the most important should be found. This information can come from the results section of the paper, especially in the sections highlighting the molecular interactions of the inhibitor (cite cathg), or in the section indicating the change in IC50 when certain residues are mutated (cite hivrt). It is best to consider the most important interactions and have the SMARTS expression represent the fragment that covers those key interactions.
Cathg
