First+100+Targets

The 218 anti-malaria target compounds have been docked to the [|enoyl reductase protein] (picture courtesy of [|Find-A-Drug]) using the THINK software. A screen shot of [|UC0010] docking, with the interacting amino acids highlighted in blue, can be seen [|here]. Also, a picture of the molecule with only the interacting amino acids can be seen [|here]. An [|interactive 3D view] is available via Jmol by exporting to PDB format. It would be nice if we could see the H-bonds between the protein and ligand in the Jmol view.

When the molecule is docked, a "G-Score" is included in the output, which is a measure of the free energy of the protein-ligand complex. The scoring method THINK uses can be viewed in [|this paper (Murray 2004)].

The THINK v1.32 software is available from [|Treweren].

Docking Experiments
D-EXP001 - Docking using SMILES and a provided script. D-EXP002 - Performing a 3D site search, using the number of specified centers and tolerance levels as a variant. The first five molecules of our library were used to compare the methods. D-EXP003 - Comparison of data: Script Docking, 3D Site searching (with different settings compared), and Find-A-Drug's Preliminary Data on our library of 218 molecules. D-EXP004 - Docking a few sample molecules from our library with the stereochemistry of the diketopiperazine substituents explicitly defined. D-EXP005 - Docking of the possible analogs synthesized in Exp052, Exp054, and Exp063 as cyclized, BOC protected and deprotected. D-EXP006 - Attempting to dock the molecules from D-EXP004 as their uncyclized precursors (protected and deprotected). (**Aborted**) D-EXP007 - Docking a DKP library provided to use by NCH Labs. D-EXP008 - Comparison of results of a collaborator with our results on DEXP005 (**Aborted**) D-EXP009 - Docking of the molecules in the [|Usefulchem Molecules blog]. (**Aborted**) D-EXP010 - Anti-tumor property prediction of 68K CombiUgi library D-EXP011 - To dock CombiUgi Library 2 (500K) against enoyl reductase using Fred. D-EXP012 - To dock CombiUgi Library 2 (500K) against falcipain-2 using Fred. D-EXP013 - Rank a virtual library of Ugi products using Rajarshi Guha's algorithm predicting anti-tumor activity. D-EXP014 - Docking library UClib003 in pockets V1 and V2 of[| Falcipain-2] - (71K) D-EXP015 - To dock CombiUgi UClib005 (1512 compounds) against falcipain-2 using the covalent docking option of GOLD. This library has chloroacetic acid as a common component to serve as the electrophile in the irreversible docking. D-EXP016 - To dock CombiUgi Library 3 (71K) against Sortase using Hex (version 5.1). All of the compounds in this library have starting materials in abundance in the Bradley lab. See D-EXP014 for a similar docking run against falcipain-2 using Fred. D-EXP017 - To Dock Library 7 against targets from the ChEMBL StARlite database using fingerprints. D-EXP018 - To Dock Library 7 (15.7 Mb, 117450 Ugi products) - starting materials in abundance in the Bradley lab (07/22/2009) - against tubulin to find alternatives to taxol (paclitaxel) at ORU using vina. D-EXP019 - Rational drug design to find a Ugi product that docks in tubulin to find alternatives to paclitaxel. D-EXP020 - **(collaboration)** To Dock Library 7 (15.7 Mb, 117450 Ugi products) - starting materials in abundance in the Bradley lab (07/22/2009) - against tubulin to find alternatives to taxol (paclitaxel) at the Swiss Institute of Bioinformatics using SwissDock. D-EXP021 - To dock library 10 (570 imines and 570 amines) against tubulin using vina on ORU's cluster. @D-EXP022 - To dock library 12 (325 d ibenzalacetone derivatives ) against tubulin using PaDEL-ADV ---

A big thanks Keith Davies at [|Find-A-Drug] for his help and advice!

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