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:
- Virtual screening for three different target proteins,
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.
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