Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures

By P. Hawkins, Anthony Nicholls. Journal of Chemical Information and Modeling, 2012

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Blind prediction of solvation free energies from the SAMPL4 challenge (2014, methodology): “from the ZINC processing pipeline [24] for hydration free energy predictions, with conformations predicted by OpenEye’s Omega [8, 25, 26].”
Torsional Diffusion for Molecular Conformer Generation (2022, methodology): “Among cheminfor-matics methods, we evaluate RDKit ETKDG [Riniker and Landrum, 2015], the most established open-source package, and OMEGA [Hawkins et al., 2010, Hawkins and Nicholls, 2012], a commercial software in continuous development.”
GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles (2021, methodology): “OMEGA [Hawkins et al., 2010, Hawkins and Nicholls, 2012, Friedrich et al., 2017], a rule-based method, is one of the most established commercial software, with more than a decade of continuous development.”
Fast Docking on Graphics Processing Units via Ray-Casting (2013, methodology): “The first involves downloading the ligand in the SMILES format from the ZINC database [40], then creating a pdb format file with multiple conformers with using the Omega software [41–43] as follows:”