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.
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.
References
- Assessing the performance of OMEGA with respect to retrieving bioactive conformations, J. Boström, J.R. Greenwood, J. Gottfries. J. Mol. Graphics and Mod. 2003, 21, 449-462.
- Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding, E. Perola and P.S. Charifson. J. Med. Chem. 2004, 47, 2499-2510.
- Comparison of Comformational Analysis Techniques to Generate Pharmacophore Hypotheses Using Catalyst, R. Kristam, V.J. Gillet, R.A. Lewis and D. Thorner. J. Chem. Inf. Model. 2005, 45, 461-476.
