TAUTOMER / PROTOMER ENUMERATION & CHARGE ASSIGNMENT

Quacpac TK

Quacpak TK 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 TK 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 TK'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.

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.

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

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

For more detailed information on Quacpac TK, check out the link below:

Documentation

Cheminformatics

The Cheminformatics suite of toolkits provides the core foundation upon which all the OpenEye applications and remaining toolkits are built.

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.

OEChem TK Core chemistry handling and representation as well as molecule file I/O
FastROCS™ TK Real-time shape similarity for virtual screening, lead hopping & shape clustering
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