OpenEye scientific software

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

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. 

M.J.K is supported by a National Science Foundation graduate fellowship. J.H. is supported by the sixth Framework Program of the European Commission. We are grateful to MDL Information Systems Inc. for the MDDR database Daylight Chemical Information Systems Inc. and OpenEye Scientific Software for software support. We thank John J. Irwin for reading the manuscript and Brian K. Shoichet for mentoring. 

OpenEye Scientific Software http //www.eyesopen.com/products/applications/fred.html CAChe Software http //www.cachesoftware.com/biomedcache ... 

In EON [33], also from OpenEye Scientific Software, the Poisson-Boltzmann equation is solved to calculate the electrostatic potential on the nodes of a 3 D grid constructed around a molecule. The molecule has MMEE94 nuclei-centered charges assigned. The OpenEye Electrostatic Tanimoto (OEET) similarity is given by... 

OpenEye Scientific Software, Inc., 9 Bisbee Court Suite D, Santa Fe,... 

BROOD v2.0, OpenEye Scientific Software Inc., http //eyesopen.com/documentation. 

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