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OpenEye's portfolio of molecular modeling applications is presented as a workflow involving ligand- and structure-based design strategies. FILTER and QUACPAC prepare the input compounds by removal of undesirables and application of a variety of charge models. Next, OMEGA generates high quality 3D conformer ensembles. ROCS searches compound libraries for 3D shape (and chemistry) similar molecules. EON may then be used to refine the ROCS hits by electrostatic similarity. BROOD searches fragment databases for bioisosteric replacements using similar approaches to ROCS and EON. FRED is OpenEye's docking and scoring application. Hit structures may then be optimized with SZYBKI. VIDA is a powerful graphical interface for visualization and effective communication of results, which VIVANT can then export live into PowerPoint® presentations or web pages. AFITT is a standalone application for ligand fitting to crystallographic density.

Toolkits are programming libraries for creating customized applications with object-oriented accessibility to a given set of capabilities. Central to the portfolio is OEChem TK, OpenEye's programming library for chemistry and cheminformatics, on top of which a number of other toolkits have been built. Among the six modeling toolkits, four (Quacpac TK, Omega TK, Shape TK and Szybki TK) have been made partially available as applications, while two are only available as toolkits (Zap TK and Spicoli TK). There are also four additional cheminformatics toolkits beyond OEChem (GraphSim TK, MolProp TK, Lexichem TK and OEDepict TK). All the toolkits are written in C++ and have a stable, documented API. Functionality is also accessible via Python and Java wrappers.