GEMDOCK : molecular docking tool

GEMDOCK - a Generic Evolutionary Method for molecular DOCKing GEMDOCK is a program for computing a ligand conformation and orientation relative to the active site of target protein. The tool was developed by Jinn-Moon Yang, a profesor of the Institute of Bioinformatics, National Chiao Tung University. The performance of GEMDOCK has been evaluated on several terms: The accuracy of molecular docking and the screening utility were better than other docking methods. These results have been published.

The main features of GEMDOCK were

  • Scoring function: an empirical scoring function having fewer local minima to replace the relatively complicated AMBER-based energy function.
  • Evolutionary algorithm: a differential evolution operator to reduce the disadvantages of Gaussian and Cauchy mutations, and a new rotamer-based mutation operator to reduce the search space of ligand structure conformations.
  • GEMDOCK may be run as either a purely flexible or hybrid docking approach.
  • GEMDOCK is an automatic system that generates all related docking variables, such as atom formal charge, atom type, and the ligand binding site of a protein.