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CONFORMER ENSEMBLES CONTAINING BIOACTIVE CONFORMATIONS

OMEGA for Conformation Generation

The most widely used and highly cited conformation generation tool in the world, OMEGA robustly samples conformational space at high speed across a wide range of medicinally relevant chemical space from traditional drug-like molecules to macrocycles.

Proven effective at reproducing bioactive conformations and supporting virtual screening at ultra-large scale, it provides both high speed and excellent accuracy.

Conformations generated with OMEGA serve as input to a variety of applications including 3D similarity tools, docking engines, and machine learning methods.

Trusted for its unmatched combination of speed and accuracy, OMEGA is the gold standard for conformation generation and the tool of choice for computational chemists across industry and academia.

Omega reproduction
OMEGA's reproduction of a high-quality ligand structure from the PDB.

Features

  • Flexible sampling methods. Exhaustive or Bayesian sampled torsion driving for drug-like molecules and distance geometry for macrocycles.
  • Sampling at speeds of 50 msec/molecule or less.
  • User-configurable search resolution.
  • Automatic superposition of structural features.
  • Excellent reproduction of solid-state and solution conformations of drug-like molecules and macrocycles.
  • Distributed processing via MPI for all supported platforms.
Omega_Exhaustive_vs_Bayesian_Speedup
Achieve a 2-3X speedup with Omega Bayesian sampling. Time comparison based on a dataset of 39K compounds from multiple sources.

The Gold Standard. Now Faster. 

OMEGA's torsion driving algorithm has been enhanced with Bayesian sampling that intelligently focuses conformer generation on low-energy structures. Rather than exhaustively enumerating all torsion angle combinations, the algorithm continuously refines sampling probabilities based on conformational energy landscape explored up to that point, delivering a 2–3x speedup over exhaustive enumeration. 

Combined with OMEGA's GPU implementation, Bayesian sampling provides an additional 1.5x acceleration, making high-quality conformer generation faster and more scalable than ever for large compound libraries. 

OMEGA with AI. Speed without Compromise.

This performance gain does not come at the cost of quality. OMEGA with Bayesian sampling reproduces bioactive conformations with 80% of ligands within 1Å RMSD the experimental conformation across 6,000 PDB structures with HT (Highly Trustworthy) Iridium scores. Structure-based virtual screening performance is equivalent to that obtained from exhaustive sampling.

OMEGA_Image_RMSD
Conformational ensembles generated by OMEGA enhanced with Bayesian bandit approach with Thompson sampling accurately reproduce bioactive conformations. Validated against 6,000 PDB crystal structures, 80% of ligands are reproduced within 1Å RMSD of the crystal structure.

Learn more

OpenEye's OMEGA produces high-quality ensembles of bioactive conformations with the fastest speed when compared to other commercially available conformer generators for drug-like molecule.

See how OMEGA samples conformational space accurately and at high speed in this webinar (August 2023) by Paul Hawkins, Ph.D 

References

  1. Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database, Hawkins, P.C.D., Skillman, A.G., Warren, G.L. Ellingson, B.A. and Stahl, M.T., J. Chem. Inf. Model., 2010, 50, 572-584.
  2. Conformer generation with OMEGA: Learning from the dataset and analysis of failures, Hawkins, P.C.D., Nicholls, A.N., J. Chem. Inf. Model., 2012, 52, 2919-2936.
  3. Conformational Analysis of Drug-like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding, Perola, E. and Charifson, P.S., J. Med. Chem. 2004,47, 2499-2510.
  4. High-Quality Dataset of Protein-Bound Ligand Conformations and its Application to Benchmarking Conformer Ensemble Generators, Friedrich, N.-O., Meyder, A., de Bruyn Kops, C., Sommer, K., Fachsenberg, F., Rarey, M., Kirchmair, J. J. Chem. Inf. Model. 2017, 57, 529-539.
  5. Benchmarking Conformer Ensemble Generators, Friedrich, N.-O. de Bruyn Kops, C. Fachsenberg, F. Sommer, K., Rarey, M. Kirchmair, J. J. Chem. Inf. Model. 2017, 57, 2719-2728.
  6. Decisions with Confidence: Application to the Conformation Sampling of Molecules in the Solid State, Hawkins, P.C.D., Wlodek, S., J. Chem. Inf. Model., 2020, 60, 3518-3533. (doi: 10.1021/acs.jcim.0c00358)
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