Introduction

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 lead compounds.

Download :
iGEMDOCK is available for free on non-commercial researches.

  • iGEMDOCK v2.1

  • iGEMDOCK v2.0

  • iGEMDOCK v1.0

  • 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:
    Docking/screening module Post-analyzing module

    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

      Example command:
      >cd /home/user/Desktop
      >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.

      Example command:
      >cd ./iGEMDOCKv2.1-centos/bin
      >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)

      >./iGemdock

      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)
      >./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)

      >LD_LIBRARY_PATH=/home/user/Desktop/iGemdockv2.1-centos/bin
      >export LD_LIBRARY_PATH
      >./iGemdock
    Support / Download

    Support :

    • If you need help to install iGEMDOCK on your computer or want to suggest new features or improvements, please contact us.

    Download :

    • System requirements: iGEMDOCK needs to be installed in a Windows or Linux.

    • iGEMDOCK is available for free on non-commercial researches.

    • Get iGEMDOCK (download)