Toolkit Development Platform

Quacpac TK

Quacpac TK

Tautomer / Protomer Enumeration & Charge Assignment

QUACPAC offers everything necessary to do charges well. As the chemistry of molecular interactions is a matter of shape and electrostatics, accurate or at least consistent charge representation is critical in drug design. However, even the best charge models are of limited value if protonation states are wrong.

QUACPAC provides pKa and tautomer enumeration in order to get correct protonation states. It also offers multiple partial charge models (including MMFF94 [1], AM1-BCC [2], and AMBER [3]) that cover a range of speed and quality in order to allow appropriate charging for every end use.

QUACPAC's approach to tautomeric enumeration is to provide multiple tautomeric states rather than one "correct" tautomer. Subsequent downstream processes are then used to identify the appropriate tautomeric form.

Features

  • Protonation state enumeration for pH 2-14
  • Tautomer enumeration and canonicalization
  • Gasteiger and MMFF94 [1] partial charges at about 1000 molecules per second
  • HF/6-31G* quality charges with AM1-BCC [2] at 1 molecule per second for drug-sized molecules
  • Set a single favorable ionization state for pH=7.4
For more detailed information on Quacpac TK, check out the links below:


 Documentation   >   Evaluate
Electrostatic potential around a collagenase inhibitor when it is charged using the AM1-BCC and Gasteiger models. Appropriate charging is critical for accurate calculations and meaningful visualizations.

Electrostatic potential around a collagenase inhibitor when it is charged using the AM1-BCC and Gasteiger models. Appropriate charging is critical for accurate calculations and meaningful visualizations.

Graphs comparing the accuracy of the AM1-BCC and Gasteiger charge models for reproducing experimental measurements.

Graphs comparing the accuracy of the AM1-BCC and Gasteiger charge models for reproducing experimental measurements.

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