Conformer Ensembles Containing Bioactive Conformations

OMEGA was designed for use with the large libraries required for computer-aided drug design. It generates multi-conformer structure databases with high speed and reliability.

OMEGA performs rapid conformational expansion of drug-like molecules, yielding a throughput of tens of thousands of compounds per day per processor.

OMEGA is very effective at reproducing bioactive conformations [1], and provides an optimal balance between speed and performance when used on large compound databases [2].

OMEGA conformational databases can be used as input to a variety of applications including docking engines (FRED), shape comparison tools (ROCS) and pharmacophore perception algorithms.

OMEGA's knowledge-based approach produces databases of comparable quality to much more computationally expensive methods [3].

The Xray crystal structure of Lipitor in its active conformation (green) overlaid by an OMEGA
conformation which reproduces the active conformation to within 0.75 Angstrom rmsd.

Features

• Very rapid (1-2 sec/molecule), systematic and rule-based conformer search
• Converts from 1D or 2D to 3D using distance bounds methods
• Diverse ensemble selection based on RMS distance and strain energy
• User-configurable search resolution
• Automatic superposition of structural features
• Distributed processing via PVM for most Unix platforms

For OMEGA 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] Boström, J., Greenwood J.R., and Gottfries, J., J. Mol. Graph. Mod., 2003, 21, 449.
[2] Perola, E. and Charifson, P.S., J. Med. Chem., 2004, 47, 2499.
[3] Kristam, R., Gillet, V. J., Lewis, R. A., Thorner, D., J. Chem. Inf. Model. 2005, 45, 461.

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