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OMEGA

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.

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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