Toolkit Development Platform

MolProp TK

MolProp TK

The MolProp TK provides a customizable framework for molecular property calculation geared towards enabling rapid database filtering. Filtering attempts to eliminate inappropriate or undesirable compounds from a large set before beginning to use them in modelling studies. The goal is to remove all of the compounds that should not be suggested to a medicinal chemist as a potential hit. This exercise is obviously case dependent, depending on ease of the assay, intended target, personal bias of the modeller & medicinal chemist, strengths of the company, etc. which makes this problem one that is highly amenable to a toolkit solution.

The criteria for passing or failing a given molecule fall into three categories:

Physical properties

  • Molecular weight
  • Topological polar surface area (TPSA)
  • logP
  • Bioavailability

Atomic and functional group content

  • Absolute and relative content of heteroatoms
  • Limits on a very wide variety of functional groups

Molecular graph topology

  • Number and size of ring systems
  • Flexibility of the molecule
  • Size and shape of non-ring chains

Beyond the standard molecular properties available from OEChem TK such as molecular weight and atom type counts, MolProp TK calculates XlogP [1], XlogS, and PSA [2]. There is also a variety of ADME filter available such as Lipinski [3], Egan [4], Veber [5] and Martin [6]. In addition to calculating properties and filtering on those properties, MolProp TK provides a variety of preprocessing tools for metal and salt removal, pKa normalization, normalization, reagent selection and type checking.

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


 Documentation   >   Evaluate

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

References

  1. A New Atom-Additive Method for Calculating Partition Coefficients Wang, R., Ying, F., Lai, L.J., Chem. Info. Comput. Sci., 1997, 37, 615.
  2. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties Ertl, P., Rohde, B., Selzer, P., J. Med. Chem., 2000,37, 3714.
  3. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Lipinski, C., et. al., Adv. Drug. Deliv. Rev., 1997, 23, 3.
  4. Prediction of drug absorption using multivariate statistics Egan, W.J., Merz, K.M., Baldwin, J.J., J. Med. Chem., 2000, 43, 3867.
  5. Molecular properties that influence the oral bioavailability of drug candidates Veber, D.F., Johnson, S.R., Cheng, H.Y., Smith, B.R., Ward, K.W., Kipple, K.D., J. Med. Chem., 2002, 45, 2615.
  6. A bioavailability score Martin, Y.C., J. Med. Chem., 2005, 48, 3164.