D-EXP001

=Objective= To provide some insight on how the docking procedure works using THINK 1.32 software, to begin getting an idea of how the software works and what the ouput means.

=Procedure= A [|script] containing a list of SMILES generated from this [|Chemsketch file] is called upon to dock to the [|enoyl reductase protein]. ([|screencast]). The docking process takes only a few minutes per molecule. A few are blown up too large for the page and are unreadable, so they are consequently not included in the data.

=Results= The data of the first 100 molecules are presented in [|Microsoft Excel format]. Each page of the .pdf file shows a different molecule, which is it's number designation in the first column (i.e. page 20 of the .pdf number 20 in the first column). The second column describes whether or not the molecule docked to the protein, and the third column shows the Gibbs' Free Energy (the "score") of the interaction.

=Discussion= Most of the compounds docked, and the few that didn't may be attributed to a minimum threshold in the console script bring used to define a molecule as a "hit". It is also possible that the inability to reproduce docking in some cases is due to minimization to a structure with different chirality, one that SMILES doesn't immediately exploit. The process of extracting SMILES code for each molecule from Chemsketch is very slow. In the future batch conversion software such as OpenBabel should be used.

Conclusion
This method seems good to test a small set of molecules, or a few to compare side by side to one another. Upon viewing the script, it is providing these settings for THINK to use in a 3D site search, just for an individual molecule: File> Preferences> Pharmacophores> WARP SPEED = 1, RE-USE RESIDUES.

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