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OEDocking TK

There are a wide variety of docking programs available to the community at large; however, until now there have been no resources in existence for individual methods developers to provide a common and well supported foundation for the development of new docking and scoring applications.

The OEDocking TK from OpenEye is a new programming library that provides this core docking and scoring functionality. Coupled with the highly acclaimed cheminformatics functionality in OEChem, the OEDocking TK is an obvious choice for anyone seeking to develop new docking tools. The initial release of the toolkit supports docking, scoring, and optimization with the Chemscore, Chemgauss3, PLP, and Shapeguass scoring functions. The ligand-aware Hybrid Docking functionality unique to OpenEye's FRED docking program is also provided in the toolkit. C++, C#, Python, and Java are supported.

Docking Features

  • Exhaustive search followed by pose optimization
  • Hybrid docking (uses the structure of a known bound active to guide docking)
  • Docking constraints

Scoring Features

  • Score optimization (systematic solid body optimization)
  • Break down of score by atom and/or scoring function component
  • Score annotation (scores are stored on molecule for visualization in VIDA

Scoring Functions

  • Chemgauss3
  • Chemscore
  • PLP
  • Shapegauss

Bibliography

  • Mark McGann, Harold R Almond, Anthony Nicholls, J. Andrew Grant and Frank K. Brown, Gaussian Docking Functions, BioPolymers, Vol. 68, pp. 76-90, 2003.
     
  • Gennady M. Verkivker, Djamal Bouzida, Daniel K. Gehlaar, Paul A. Rejto, Sandra Arthurs, Anthony B. Colson, Stephan T. Freer, Veda Larson, Brock A. Luty, Tami Marrone and Peter W. Rose, Deciphering common failures in molecular docking of ligand-protein complexes, Journal of Computer-Aided Molecular Design, Vol. 14, pp. 731-751, 2000.
     
  • Matthew D. Eldridge, Christopher W. Murray, Timothy R. Auton, Gaia V. Paolini and Roger P. Mee., Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes, Journal of Computer-Aided Molecular Design, Vol. 11, pp. 425-445, 1997.