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For Immediate Release
Santa Fe, NM, August 17, 2004 - OpenEye Scientific Software, Inc. is pleased to announce the release of QUACPAC 1.1, a suite of programs that generates high-quality charge states and charges for both small molecules and proteins. OpenEye's fundamental philosophy is that the chemistry of molecular interactions is a matter of shape and electrostatics. In order to do electrostatics well, the correct protonation states and accurate charges are required. "I got sick of people saying that PB does not work, when in fact they used bad charges," says Anthony Nicholls, founder of OpenEye. "QUACPAC offers everything necessary to do charges right!" QUACPAC includes pKa state and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and quality, and electrostatic potential map construction and storage.
QUACPAC highest quality partial charges are obtained for ligand molecules using the AM1-BCC model, which was designed by Dr. Christopher Bayly at Merck Frosst to reproduce HF/6-31G* quality charges at a much faster rate - about 1 molecule per second for drug-sized molecules. Such speeds are not sufficient for some screening purposes, so QUACPAC also offers the VC2003 and MMFF partial charges models, which can process about 400 and 1000 molecules per second, respectively.
QUACPAC's pKa program seeks to enumerate all of the pKa states that fall in the range of 2-14 in aqueous solvent. This ensemble includes the ground state plus all charge states within 8 kcals, a range similar to that used for generating conformational ensembles of small molecules. This ensures that all reasonable pKa states will be in the ensemble for subsequent screens. Similarly, QUACPAC can enumerate all tautomeric states for a given compound. For proteins, QUACPAC determines pKa via Poisson-Boltzmann (PB) electrostatics.
"Perhaps one of the most novel components of QUACPAC is the ability to handle PREPS," continues Nicholls. PREPS, for Polynomial Representation of Electrostatic Potential Surfaces, is a compact method of storing through-space potential distributions, in a 184-character string, so that they may be attached to any molecule's structure file. "PREPS lets you calculate the electrostatic potential once and store it on the molecule, so it can be quickly used on the fly, rather than having to be recalculated. This puts electrostatic potentials on the same footing as other chemical properties."
About OpenEye
OpenEye Scientific Software was founded in 1997 to develop large-scale modeling applications and toolkits. Primarily geared towards drug discovery and design, areas of application include structure generation, docking, shape comparison, charge and electrostatics, chemical informatics and visualization. The software is designed for scientific rigor, as well as speed, scalability and platform independence. OpenEye makes most of its technology available as toolkits - programming libraries suitable for custom development. OpenEye software typically is distributable across multiple processors with PVM, supports 64-bit processing, and runs on Linux, Windows and Mac, as well as HP/Compaq, IBM, SGI and SUN flavors of UNIX.
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