SZYBKI Enables Entropy Calculations in Various Environments, as Well as Several Other New Features, in the 1.5.0 Release of the Molecular Structure Optimization and Virtual Screening Application from OpenEye Scientific Software
SANTA FE, N.M.–(BUSINESS WIRE)–OpenEye Scientific Software, Inc. (www.eyesopen.com), the developer of innovative molecular modeling and cheminformatics solutions for drug discovery, announces the release of SZYBKI 1.5.0, the company’s molecular structure optimization application.
SZYBKI optimizes molecular structures using the Merck Molecular Force Field, either with or without solvent effect, to yield quality 3D molecular structures for use as input to other programs. Since the chemistry of molecular interactions is a matter of shape and electrostatics, it is impossible to consider either without reasonable 3D molecular structures.
SZYBKI can also refine portions of a protein structure and optimize ligands within a protein active site, making it a particularly useful adjunct to docking programs, such as FRED from OpenEye.
Significant to the release of SZYBKI 1.5.0 is the ability to perform ligand entropy calculations in different environments based on the methods described in the recently published paper “Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian” (J. Chem. Theory Comput., 2010, 6 (7), pp 2140–2152) written by Dr. Stanislaw Wlodek, Senior Scientist at OpenEye Scientific Software and author of SZYBKI. Wlodek states, “With this new SZYBKI release we offer for the first time entropy calculations for ligands in different environments. This is a significant and necessary step toward the ultimate goal of accurate estimation of binding free energy.”
Other important new features of SZYBKI 1.5.0 include:
- The ability to handle certain classes of divalent selenium compounds, including selenols (RSeH) and certain specific selenides (RSeR1).
- SZYBKI no longer attempts, by default, to assign the “closest” MMFF94 atom type to atoms for which a unique MMFF94 type could not be found. This feature is still available but must be specified by the user.
- Reported ligand RMSD values can now optionally refer to the heavy atoms only.
- Faster calculation of default VdW protein-ligand potential in the active site via the use of lookup tables. Exact VdW protein-ligand potentials can still be calculated if desired.
A complete list of all the new SZYBKI features can be seen at http://www.eyesopen.com/products/applications/szyki.html.
ABOUT OPENEYE SCIENTIFIC SOFTWARE
OpenEye Scientific Software Inc. is a privately held company headquartered in Santa Fe, New Mexico, with offices in Boston, Massachusetts, Strasbourg, France and Tokyo, Japan. It was founded in 1997 to develop large-scale molecular modeling applications and toolkits. Primarily aimed toward drug discovery and design, areas of application include:
- chemical informatics
- structure generation
- docking
- optimization
- shape comparison
- electrostatics
- crystallography
- 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, supports 64-bit processing, and runs on Linux, Windows and Mac OS X, as well as IBM and SUN flavors of UNIX. For further information on the company and its products, see www.eyesopen.com.
