Molecular Structure Optimization in situ with MMFF94

SZYBKI [1] optimizes molecular structures with 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 also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.

In situ optimization of a ligand with SZYBKI.	Accurate Poisson—Boltzmann vs. Sheffield Solvation Model solvation energies for a database of 64,000 drug-like molecules [3].

Features

• MMFF94 and MMFF94s energies or optimized geometries; atom types, energies and gradients strictly validated against Merck's published dataset [2]
• Solvent effects with ZAP's Poisson-Boltzmann model or the Sheffield model [3] for binding energies and geometry optimization
• Flexibility of protein active-site polar hydrogens or side-chains
• Ligand optimization within the field of a protein active site
• Gradient minimization in several coordinate frames (Cartesian, torsional, rigid body)
• Fully optimizes (gas phase) about 200 drug-sized molecules per minute
• Optionally excludes various terms from potential when determining energy and gradient
• Constrains coordinates (fixed atoms or harmonic constraints)
• Distributing processing via PVM for most Unix platforms

For SZYBKI and All OpenEye Products

• Multiple file format handling: robust reading and specification-compliant writing of: SMILES, SLN, SDF, MOL, MOL2, PDB, FASTA, MOPAC, MacroModel, XYZ, CCP4, XPLOR, and OEBinary.
• Platform independence: support for Linux, Windows, Mac OS X and many flavors of Unix in both 32 and 64 bit.

[1] Szybki (shib´·kee) means "fast" in Polish.
[2] Halgren, T.A., J. Comp. Chem, 1996, 17, 490; Halgren, T.A., J. Comp. Chem, 1999, 20, 720.
[3] Grant, J.A., Pickup, B.T., Sykes, M.J., Kitchen, C.A., Nicholls, A., Chem. Phys. Lett., 2007, 441, 163.