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istar: a web platform for large-scale protein-ligand docking.

Hongjian Li1, Kwong-Sak Leung1, Pedro J Ballester2

  • 1Department of Computer Science and Engineering, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.

Plos One
|January 30, 2014
PubMed
Summary
This summary is machine-generated.

We developed istar, a web platform for automated protein-ligand docking using the enhanced idock 2.0 engine. istar offers faster and more accurate docking than existing tools, aiding drug discovery.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • Protein-ligand docking is crucial for identifying drug candidates.
  • Automating large-scale docking is essential for efficient drug discovery pipelines.
  • Existing online docking platforms often lack advanced features for analysis and usability.

Purpose of the Study:

  • To develop a publicly accessible web platform, istar, for automated large-scale protein-ligand docking.
  • To enhance the idock docking engine to version 2.0, improving speed and accuracy.
  • To integrate RF-Score for binding affinity prediction and provide advanced visualization and analysis tools.

Main Methods:

  • Collected 17,224,424 ligands from the ZINC database.
  • Revamped the idock docking engine to version 2.0 with improved performance and integrated RF-Score.
  • Conducted benchmark studies comparing idock 2.0 against AutoDock Vina 1.1.2 using PDBbind and CSAR datasets.
  • Developed the istar web platform with features for ligand filtering, job monitoring, and results visualization.

Main Results:

  • idock 2.0 demonstrated comparable success rates to AutoDock Vina but was 8.69 to 37.51 times faster.
  • The istar platform, combined with RF-Score, achieved high correlation coefficients (up to 0.859) between predicted and experimental binding affinities on the PDBbind 2012 core set.
  • istar provides features like real-time job monitoring and detailed output analysis, surpassing other online docking platforms.

Conclusions:

  • The istar platform and idock 2.0 offer a significant advancement in automated, large-scale protein-ligand docking.
  • istar streamlines the drug discovery process by providing a user-friendly interface with powerful computational tools.
  • The enhanced speed and accuracy of idock 2.0, coupled with istar's features, make it a valuable resource for researchers in computational chemistry and drug discovery.