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QUACPAC specifications


Unique identifier OMICS_33648
Alternative name Quality Atomic Charges, Proton Assignment, and Canonicalization
Software type Application/Script
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS, Windows
License Commercial
Computer skills Advanced
Version 1.7.0
Stability Stable
Registration required Yes
Maintained Yes


No version available


  • person_outline Benjamin Ellingson

Additional information


Publication for Quality Atomic Charges, Proton Assignment, and Canonicalization

QUACPAC citations


QSAR Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities

Front Pharmacol
PMCID: 5845645
PMID: 29559909
DOI: 10.3389/fphar.2018.00146

[…] tomic charges: the empirical method of Gasteiger-Hückel available on SYBYL-X v.1.2 (SYBYL-X 1.2, Tripos International, St. Louis, MO, United States) and the semi-empirical AM1-BCC (, ) implemented in QUACPAC v. (QUACPAC OpenEye Scientific Software, Santa Fe, NM, United States2). The protonation state of the molecules were performed at pH 7.4, using QUACPAC 1.6.3 (QUACPAC O […]


Oxidative stress via inhibition of the mitochondrial electron transport and Nrf 2 mediated anti oxidative response regulate the cytotoxic activity of plumbagin

Sci Rep
PMCID: 5773707
PMID: 29348410
DOI: 10.1038/s41598-018-19261-w

[…] ,4 naphthoquinone [CID8530] were downloaded from PubChem (3D SD format) and assigned partial charges using OpenEye’s molcharge utility (MOL2 format) with the MMFF method (OpenEye Scientific Software, QUACPAC v1.6.3.1). The program Smina, a fork of AutoDock Vina v1.1.2, was used for ligand docking using the default search parameters and scoring function,. To designate a search space to explore arou […]


Combined Virtual and Experimental Screening for CK1 Inhibitors Identifies a Modulator of p53 and Reveals Important Aspects of in Silico Screening Performance

Int J Mol Sci
PMCID: 5666784
PMID: 28984824
DOI: 10.3390/ijms18102102

[…] nation state, tautomerization, stereoisomer representation, and conformer generation (for ROCS only) using tools provided by the corresponding screening packages (LigPrep module for Glide and Filter, Quacpac, Omega for ROCS). Omega was used with a limit of 200 conformers generated for each molecule. Concerning Glide, prior to grid generation, all protein structures were prepared by using the Prote […]


Discovery and Optimization of a Selective Ligand for the Switch/Sucrose Nonfermenting Related Bromodomains of Polybromo Protein 1 by the Use of Virtual Screening and Hydration Analysis

J Med Chem
PMCID: 5301280
PMID: 27617704
DOI: 10.1021/acs.jmedchem.6b00355

[…] ing the LigPrep routine (Schrödinger Inc.). The NCI/DTP collection was prepared independently for ROCS screening using the enumeration and conformer generation tools provided by OpenEye Inc. (Filter, Quacpac, Omega) with default settings. The ligand-based approach was based on the ROCS algorithm (OpenEye Inc.) with the Tanimoto-combo scoring scheme and the implicit Mills–Dean force field, while 1 […]


A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor

Nucleic Acids Res
PMCID: 5041483
PMID: 27536006
DOI: 10.1093/nar/gkw687

[…] and binding pocket of DoubleMut-IBD model and the ‘holo’ model with the best ligand–protein interface score was selected. Partial charges on the molecules were determined using AM1-BCC application in QuacPac package, version 1.3.1 of OpenEye Scientific Software (Santa Fe, NM). […]


Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein Protein Interactions

PLoS One
PMCID: 4617380
PMID: 26484863
DOI: 10.1371/journal.pone.0140359
call_split See protocol

[…] rotonation state for each native ligand, in the context of the protein-ligand complex. By contrast, the most likely tautomeric state / protonation state for the decoy ligands was determined using the QUACPAC toolkit [], in the absence of the protein. We note that for a real virtual screening application, the native ligand’s tautomeric state / protonation state in the protein environment would not […]


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QUACPAC institution(s)
OpenEye Scientific Software, Santa Fe, NM, USA

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