Toolkit Development Platform

Zap TK

Zap TK

Programming Libraries for Molecular Modeling

Zap TK produces Poisson-Boltzmann electrostatic potentials [1] and, from them, biologically interesting properties including solvent transfer energies, binding energies, pKa shifts, solvent forces, electrostatic descriptors, surface potentials and effective dielectric constants. Zap TK works well for small molecules, proteins and macromolecular ensembles [2]. Unique to Zap TK is a dielectric function based on atom-centered Gaussians [3], which avoids the pitfalls of discrete dielectric constants.

In a study of LCK kinase inhibitors, Zap TK was used to analyse the ligands solvent-exposed portions, simultaneously optimizing the solubility and binding affinity. In another study, Zap TK was used for high-throughput MM-PBSA calculations of relative binding free energies [4].

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


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Image Map

The OpenEye Toolkit Ecosystem

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