iGEMDOCK - A Graphical Environment for Recognizing Pharmacological Interactions and Virtual Screening
Pharmacological interactions are useful for identifying lead compounds and understanding ligand binding mechanisms
for a therapeutic target. Currently, these interactions are often inferred from a set of active compounds that were
acquired experimentally. Moreover, most docking programs loosely coupled the stages of structure-based virtual screening (VS)
from preparations through to post-screening analysis. An integrated VS environment, which provides the friendly interface
to seamlessly combine different-stage programs for VS and identifying the pharmacological interactions from screening
compounds, is valuable for drug discovery.
Here, we developed an easy-to-use graphic environment, iGEMDOCK, for the docking, virtual screening, and post-screening analysis.
For post-screening analysis, iGEMDOCK can enrich the hit rate and provide biological insights by deriving the pharmacological
interactions from screening compounds. The pharmacological interactions represent conserved interacting residues that often
form binding pockets with specific physico-chemical properties to play the essential functions of the target protein.
Experiment results show that the success rate of iGEMDOCK is 78% (root-mean-square derivations below 2.0 angstrom) on 305 protein-compound
complexes. For virtual screening, pharmacological interactions derived by iGEMDOCK often involve the biological functions
and enrich the hit rates on three public sets (i.e., estrogen receptor £\ for antagonists (ER) and agonists (ERA) and
thymidine kinase (TK)). We believe that iGEMDOCK is useful for understanding the ligand binding mechanisms and discovering
iGEMDOCK is available for free on non-commercial researches.
|The architecture of iGEMDOCK||
iGEMDOCK is constructed by four major modules. The docking/screening and post-analyzing modules contain several components to make the screening/analyzing procedure smoothly
Components of docking/screening module
- mod_cav : this program generates the binding site from the ligand bounded PDB file
- mod_lig : this program provides the processing flow of selected ligand and generating list
- mod_ga : this program is the main kernel (GEMDOCK) for docking/screening module. It serves the docking/screening process and predicts the bounded poses of protein-ligand complex
Components of post-analyzing module
- mod_ac : this program analyzes the atom composition and environment of each docked pose
- mod_kc : this program is k-mean cluster method. It clusters the docked poses by their interaction or atom composition descriptors
|The interface of iGEMDOCKv2.0|
The interface of iGEMDOCK is designed for a low learning-curve and friendly environment. We demonstrate iGEMDOCK for users by the snap shots.
|The interface of iGEMDOCK includes two main pages:|
In the docking/screening step, users are able to conveniently prepare their binding site from PDB complex in iGEMDOCK interface.
The progress of screening will be reported in docking/screening window. During screening or after screening procedure, users can directly
process further analyses, such as comparison by energy, and cluster by interaction or atom compoistion. The predicted complexes can be
visualized in real time.
|Cavity preparation through docking/screening module
||Show predicted complexes by selected results in post-analysis module
|Quick installation of iGEMDOCK|
For Windows users
Download iGEMDOCKv2.1.zip to your desktop
1. Decompress the iGEMDOCKv2.1.zip
2. Execute the iGemdock.exe in the folder "bin"
For Linux users
Download iGEMDOCK (e.g., iGEMDOCKv2.1-centos.tar) to your desktop. For example, download to the directory "/home/user/Desktop"
1. Change directory to your desktop and decompress the tar file
>tar -xf ./iGEMDOCKv2.1-centos.tar
2. Change to the sub-folder "bin". The folder is located in the folder of iGEMDOCK.
3. Change the authority to "755" for the files in the "bin" folder.
>chmod 755 *
4. Start iGEMDOCK (by executing iGemdock or using iGemdock.sh)
4.1. Start iGEMDOCK by executing "iGemdock" (If you have installed Qt library)
4.2. Start iGEMDOCK by executing "iGemdock.sh" or by following commands (If you do not install Qt library)
Example command: (Start from iGemdock.sh)
or >bash iGemdock.sh
4.3. Manually setup library and start iGemdock (If you do not use bash and not install Qt library)
|Support / Download|
- If you need help to install iGEMDOCK on your computer or want to suggest new features or improvements, please
- System requirements: iGEMDOCK needs to be installed in a Windows or Linux.
- iGEMDOCK is available for free on non-commercial researches.
- Get iGEMDOCK (download)