OpenEye

Fred (Openeye Software) conformational ensembles Gaussian or empirical score... 

OMEGA, OpenEye Scientific Software, Santa Ee, NM, USA, http //www. eyesopen.com. 

These unwanted functional groups can be easily encoded as SMARTS [37] to be used as structural alerts for HTS compound prioritization or compound acquisition. OpenEye s Filter [38] is an excellent example of such a filtering tool. 

FRED Fast Rigid Exhaustive Docking OpenEye www.eyesopen.com... 

Openeye Scientific Software http //en.wikipedia.org/wiki/OpenEye Scientific Software... 

OpenEye Scientific Software Inc OEChem Toolkit, Santa Fe, NM, USA, 2009. www.eyesopen.com... 

Examples of volume-based approaches by other commercial software distributors are FlexS from Tripos [78, 79] and ROCS from OpenEye [80, 81]. 

OpenEye s Lexichem,23 and ChemAxon52 has announced the imminent release of their own product early in 2008. As mentioned earlier, an Open Source Java library for the interpretation of IUPAC systematic names,34 OPSIN, has also been made available. In this chapter, most examples are based on Name=Struct and ACD/Name to Structure. We judge these programs to currently be the most advanced products in this area, but all considerations are general in nature and relevant to all of the conversion routines presently existing or still under development. 

FRED, OpenEye Scientific Software, 3600 Cerrillos Rd., Suite 1107, Santa Fe, NM 87507. 

To exemplify a molecular similarity method, we employed here a 3D shape-based molecular similarity approach using OpenEye scientific software (OpenEye). A set of 27 molecules (Amoore, 1971) were compared to benzaldehyde (query molecule). The representation used here is based on the volume of each molecule. A conformational ensemble is built for the molecules in the database, whereas the conformation of the query remains fixed (the chemical nature of benzaldehyde does not entail different conformers, though in many cases the conformation of the query molecules might be complex and crucial). After the conformers of each molecule in the data set are built, each one of them is compared with the query and a similarity value is computed. For the particular program employed here (ROCS), the similarity is quantified as a score formed by two terms, one takes into account the chemical nature of the molecules while the other relies on molecular shape, such score is referred to as combo score. The maximum similarity value is 2 which can only be obtained from the comparison of a molecule with itself in the exact same conformation (perfect match). The normalized values (from 0 to 1) for the odor and combo score similarities are compared in the graph shown in Fig. 2.4. As can be observed, as the combo score increases, the odor similarity to benzaldehyde also increases. This correlation shows that part of the odor similarity was captured by the molecular... 

The authors are thankful to Dr. Terry Peppard (Robertet Flavors, Inc.) for valuable discussions and for proof reading this book chapter. This work was supported by the State of Florida, Executive Officer of the Governor s Office of Tourism Trade and Economic Development. We thank OpenEye Scientific Software for providing OMEGA, ROCS, FRED, and VIDA programs. 

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