Drug design, interactive

S. (2010) Complexity in influenza virus targeted drug design interaction with human sialidases. Journal of Medicinal Chemistry, 53, 2998-3002. 

The interpretation of molecular surfaces is particularly important wherever molecular interactions, reactions, and properties play a dominant role, such as in drug design or in docking c.xpcrimcnts. 

The molecular surface of receptor site regions cannot be derived from the structure infoi mation of the molecule, bth represents the form ofthe active site of a protein surrounded by a ligand. This surface representation is employed in drug design in order to illustrate the volume of the pocket region or the molecular interaction layers [186. ... 

Pearlman R S and K M Smith 1998. Novel Software Tools for Chemical Diversity. Perspectives in Dn Discovery and Design vols 9/10/ll(3D QSAR in Drug Design Ligand/Protein Interactions ar Molecular Similarity), pp. 339-353. 

In general the relevance of predictions of structure-function relationships based on molecular modeling and structural bioinformatics are threefold. First they can be used to answer the question of which partners (proteins) could interact. Second, predictions generate new hypotheses about binding site, about molecular mechanisms of activation and interaction between two partners, and can lead to new ideas for pharmacological intervention. The third aim is to use the predictions for structure-based drug design. 

Bohm HJ, Schneider G, editors. Protein-ligand interactions. From molecular recognition to drug design (Vol. 19 of Mannhold R, Kubinyi H, Foikers G, editors. Methods and Principles in Medicinal Chemistry). Weinheim Wiley-VCH, 2003. 

R. P. New approaches to drug design and delivery based on drug-membrane interactions. Drug Des. Deliv. 1991, 7, 75-118. 

For a detailed description of spectral map analysis (SMA), the reader is referred to Section 31.3.5. The method has been designed specifically for the study of drug-receptor interactions [37,44]. The interpretation of the resulting spectral map is different from that of the usual principal components biplot. The former is symmetric with respect to rows and columns, while the latter is not. In particular, the spectral map displays interactions between compounds and receptors. It shows which compounds are most specific for which receptors (or tests) and vice versa. This property will be illustrated by means of an analysis of data reporting on the binding affinities of various opioid analgesics to various opioid receptors [45,46]. In contrast with the previous approach, this application is not based on extra-thermodynamic properties, but is derived entirely from biological activity spectra. 

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