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UC on ChemSpider
Alicia's Masters Thesis
Open Web Drug Dev.
To Do List
Ugi NMR Analysis
First 100 Targets
target compounds have been docked to the
enoyl reductase protein
(picture courtesy of
) using the THINK software. A screen shot of
docking, with the interacting amino acids highlighted in blue, can be seen
. Also, a picture of the molecule with only the interacting amino acids can be seen
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
- Docking using SMILES and a provided script.
- 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.
- 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.
- Docking a few sample molecules from our library with the stereochemistry of the diketopiperazine substituents explicitly defined.
- Docking of the possible analogs synthesized in
as cyclized, BOC protected and deprotected.
- Attempting to dock the molecules from D-EXP004 as their uncyclized precursors (protected and deprotected). (
- Docking a DKP library provided to use by NCH Labs.
- Comparison of results of a collaborator with our results on DEXP005 (
- Docking of the molecules in the
Usefulchem Molecules blog
- Anti-tumor property prediction of 68K CombiUgi library
- To dock CombiUgi Library 2 (500K) against enoyl reductase using Fred.
- To dock CombiUgi Library 2 (500K) against falcipain-2 using Fred.
- Rank a virtual library of Ugi products using Rajarshi Guha's algorithm predicting anti-tumor activity.
in pockets V1 and V2 of
- 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.
- 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.
- To Dock Library 7 against targets from the ChEMBL StARlite database using fingerprints.
- 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.
- Rational drug design to find a Ugi product that docks in tubulin to find alternatives to paclitaxel.
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.
- To dock library 10 (570 imines and 570 amines) against tubulin using vina on ORU's cluster.
- To dock
) against tubulin using PaDEL-ADV
A big thanks Keith Davies at
for his help and advice!
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