OpenEye Scientific Software releases SZYBKI 1.5.0 optimization application for molecular structures

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.

“Ligand Entropy in Gas-Phase, Upon Solvation and Protein Complexation. Fast Estimation with Quasi-Newton Hessian”

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.

Source : OpenEye Scientific Software

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