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
- Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database, P.C.D. Hawkins, A.G. Skillman, G.L. Warren, B.A. Ellingson and M.T. Stahl J. Chem. Inf. Model., 2010, 50, 572.
- 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.
