Primarily geared towards drug discovery and design, areas of application include conformation generation, docking, shape comparison, charge/electrostatics, cheminformatics and visualization. The software is designed for scientific rigor, as well as speed, scalability and platform independence.

OpenEye makes much of its technology available as toolkits suitable for custom development. The toolkits are available in multiple languages: C++, Python, Java and C#.^{[citation needed]}

• AFITT - Crystallographic refinement and analysis.
• BROOD - Bioisostere identification using shape, chemistry and electrostatic similarity.
• EON - Chemical similarity analysis via comparison of electrostatics overlay.
• FastROCS - Real-time 3D molecular shape searches, using GPU technology.
• FILTER - Molecular screening and selection based on physical property or functional group.
• OEDocking - Molecular docking tools including FRED (fast docking), HYBRID (ligand guided docking) and POSIT (ligand guided pose prediction).
• OMEGA - Fast, accurate conformer generation, for linear and macrocyclic molecules.
• pKa Prospector - A database of high quality pKa measurements.
• QUACPAC - Tautomers, protonation states and charges for small molecules and proteins.
• ROCS - Chemical similarity analysis via rapid 3D molecular shape searches.
• SZMAP - Identify water sites in a protein binding site for improving ligand potency.
• SZYBKI - Fast forcefield optimization of ligands in gas-phase, solution, or within a protein active site.
• VIDA - Graphical user interface that visualizes, analyzes and manages corporate collections of molecular structures and information.

Programming libraries providing other applications with object-oriented accessibility to a given set of capabilities.

• OEChem TK - Cheminformatics and 3D molecular data handling.
• OEDepict TK - Elegant 2D structure rendering of compounds.
• OEDocking TK - Docking and scoring.
• Grapheme TK - Advanced structure rendering of compounds.
• GraphSim TK - 2D molecular fingerprints and similarity calculations.
• Lexichem TK - State-of-the-art compound name and structure interconversion with support for multiple languages.
• MolProp TK - 2D molecular property calculation and filtering.
• QuacPac TK - Tautomer generation.
• Omega TK - Conformer generation.
• Shape TK - Molecular shape comparisons based on 3D overlays.
• Spicoli TK - Rapid molecular surface generation and manipulation.
• Szmap TK - Water interactions in the binding site.
• Szykbi TK - Generalized function optimization, e.g. molecular structure optimization.
• Zap TK - An efficient Poisson-Boltzmann electrostatics solver.

• Computational chemistry

• "Downloads and Upgrades: AFITT 2.3, GenBank 197.0, and the Protein Databank". BioInform. Genomeweb LLC. August 16, 2013. Retrieved August 28, 2013.
• "Company Overview of OpenEye Scientific Software, Inc". Bloomberg Businessweek. Bloomberg L.P. Archived from the original on March 5, 2009. Retrieved August 28, 2013.
• Yang, Jeremy J. (Fall 2011). "Cheminformatics Software Development: Case Studies" (PDF). Indiana University School of Informatics and Computing. Retrieved August 28, 2013.

• Official website