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TAUTOMER / PROTOMER ENUMERATION & CHARGE ASSIGNMENT

QUACPAC

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-a

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

quacpac-b

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

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.

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

Documentation

References

Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 Halgren, T. A. J. Comp. Chem, 1996 17, 490.
Fast, efficient generation of high-quality atomic charges: AM1-BCC Model. II: Parameterization and validation Jaklian, A., Jack, D.B. and Bayly, C., J. Comp. Chem, 2002, 23, 1623-1641.
Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins Cieplak, P., Cornell, W.D., Bayly, C. and Kollman, P.A., J. Comp. Chem, 1995, 16, 1357.

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