Systems biology - dynamic pathway modeling by Olaf Waulkenhour

By Olaf Waulkenhour

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By Olaf Waulkenhour

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Microarray Analysis for Mechanistic Toxicology The purpose of mechanistic toxicology consists of unraveling the genomic responses of organisms exposed to xenobiotics. Distinct experimental setups can deliver the required information. The most appropriate data analysis method depends both on the biological question to be answered and the experimental design. For the purpose of clarity, we make a Computational Biology and Toxicogenomics 53 distinction between three types of design. This subdivision is somewhat artificial and the distinction is not always clearcut.

These interaction contours are used by VolSurf to generate molecular surface descriptors which are relevant for intermolecular interactions. hydrophobic DRY probes have been used to characterize polar and hydrophobic interactions sites around thalidomide. Besides molecular volume, surface, and shape, the concentration of polar interactions on the molecular surface and the size of polar and hydrophobic interaction sites are calculated at eight energy levels. The ‘‘integy’’ (interaction energy) moment is defined in analogy to the dipole moment and describes the distance of the center of mass to the barycenter of polar or hydrophobic interaction sites at a given energy level.

Iterative partial equalization of orbital electronegativity: a rapid access to atomic charges. Tetrahedron 1980; 36:3219–3222. 21. Moreau G, Broto P. The autocorrelation of a topological structure: a new molecular descriptor. Nouv J Chim 1980; 4: 359–360. 22. Moreau G, Broto P. Autocorrelation of molecular structures. Application to SAR studies. Nouv J Chim 1980; 4:757–764. 23. Kubinyi H. The physicochemical significance of topological parameters. A rebuttal. Quant Struct-Act Relat 1995; 14:149–150.

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