Toolkit Development Platform

MedChem TK

MedChem TK

MedChem TK provides a powerful fragmentation-based analysis engine that prospectively identifies matched molecular pairs [1] that differ by both heavy-atom and hydrogen-atom substitutions. Matched molecular pairs are a compelling concept used to identify changes in properties of interest accompanying a localized structural change. Additionally, matched pair transformations provide the ability to use alternate structure sources for the generation of new leads and delta-property estimates based on the ensemble of matched structural pairs associated with each transformation.

Utilities that provide the ability to fragment structures [2] into smaller building blocks are useful for the identification and characterization of new building blocks for lead analysis or docking and evaluation. A number of different fragmentation strategies are provided to aid this activity in MedChem TK.

Additional functions are available which provide molecular complexity [3,4] metrics. Molecular complexity is useful for scoring or filtering of candidates or for clustering and ranking molecular structures.

For more information on MedChemTK, check out the links below:

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The OpenEye Toolkit Ecosystem


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


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
  SiteHopper TK Rapid Comparison of Protein Binding Sites
  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


  1. Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets, Hussain, J., Rea, C., J. Chem. Inf. Model., 2010, 50, 339.
  2. The Properties of Known Drugs: 1. Molecular Frameworks, Bemis, G.W., Murcko, M.A., J. Med. Chem. 1996, 39, 2887.
  3. The First General Index of Molecular Complexity, Bertz, S.H., J. Am. Chem. Soc., 1981, 103, 3599.
  4. Structure and Reaction Based Evaluation of Synthetic Accessiblity, Boda, K., Seidel, T., Gasteiger, J., J. Comp.-Aided Mol. Design, 2007, 21, 311.