Toolkit Development Platform

Shape TK

Shape TK

Shape TK is the basis for the ROCS application for shape-based similarity searching. The toolkit allows for fine control over optimization methods, molecule treatment and the nature of the query (grids, generic shapes). Shape TK facilitates the calculation of molecular descriptors for shape (steric multipoles), volume overlap between molecules, and spatial similarity of chemical groups (color force field), as well as the optimization of the latter two quantities.

Examples of use include aligning and comparing protein active sites, performing real-space fitting to electron density, shape fingerprinting [1], consensus shape generation, and discrimination between agonists and antagonists based on shared shapes [2].

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


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modeling-toolkits.jpg

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.

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
  Szmap TK Understanding water interactions in a bind site
  Szybki TK General purpose optimization with MMFF94
  Zap TK Calculate Poisson-Boltzmann electrostatic potentials

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

References

  1. Small molecule shape-fingerprints Haigh, J. A., Pickup, B. T., Grant, J. A., Nicholls, A., J. Chem. Inf. Model.2005, 45, 673.
  2. Scaffold hopping, synthesis and structure-activity relationships of 5,6-diaryl-pyrazine-2-amide derivatives: a novel series of CB1 receptor antagonists Boström, J., Berggren, K., Elebring, T., Greasley, P.J., Wilstermann, M., Bioorg Med Chem., 2007, 15, 4077.