Toolkit Development Platform

Omega TK

Omega TK

Omega TK offers the same features as the OMEGA application for conformer generation. Please refer to the OMEGA product page for details.

For more detailed information on Omega TK, check out the links below:


 Documentation   >   Evaluate
Example of a result obtained from a combination of modeling toolkits: conformers from Omega TK were overlain using Shape TK while surfaces and coloring were generated by Spicoli TK.

Example of a result obtained from a combination of modeling toolkits: conformers from Omega TK were overlain using Shape TK while surfaces and coloring were generated by Spicoli TK.

Cheminformatics

The Cheminformatics suite of toolkits provides the core foundation upon which all of the OpenEye applications and remaining toolkits are built. The Cheminformatics suite is a collection of seven individual yet interdependent toolkits that are described in the table below.

  Toolkit Major Functionality
  FastROCS TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
  OEChem TK Core chemistry handling and representation as well as molecule file I/O
  OEDepict TK 2D Molecule rendering and depiction
  Grapheme™ TK Advanced molecule rendering and report generation
  GraphSim TK 2D molecular similarity (e.g. fingerprints) 
  Lexichem TK  name-to-structure, structure-to-name, foreign language translation 
  MolProp TK Molecular property calculation and filtering 
  Quacpac TK Tautomer enumeration and charge assignment
  MedChem TK Matched molecular pair analysis, fragmentation utilities, and molecular complexity metrics

Modeling

The Modeling suite of toolkits provides the core functionality underlying OpenEye's defining principle that shape & electrostatics are the two fundamental descriptors determining intermolecular interactions. Many of the toolkits in the Modeling suite are directly associated with specific OpenEye applications and can therefore be used to create new or extend existing functionality associated with those applications.

  Toolkit Major Functionality
  OEChem TK Core chemistry handling and representation as well as molecule file I/O
  OEDocking TK Molecular docking and scoring
  Omega TK Conformer generation
  Shape TK 3D shape description, optimization, and overlap
  Spicoli TK Surface generation, manipulation, and interrogation
  Spicoli TK Surface generation, manipulation, and interrogation
  Spruce TK Protein preparation and modeling
  Szybki TK General purpose optimization with MMFF94
  Szmap TK Understanding water interactions in a binding site
  Zap TK Calculate Poisson-Boltzmann electrostatic potentials

References

  1. Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database, P.C.D. Hawkins, A.G. Skillman, G.L. Warren, B.A. Ellingson and M.T. Stahl, J. Chem. Inf. Model., 2010, 50, 572.
  2. Conformer generation with OMEGA: Learning from the dataset and analysis of failures, Hawkins, P.C.D., Nicholls, A.N., J. Chem. Inf. Model., 2012, 52, 2919.
  3. Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding, E. Perola and P.S. Charifson. J. Med. Chem. 2004,47, 2499-2510.
  4. Comparison of Conformational Analysis Techniques to Generate Pharmacophore Hypotheses Using Catalyst, R. Kristam, V.J. Gillet, R.A. Lewis and D. Thorner. J. Chem. Inf. Model.2005, 45, 461-476.
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