Annual Reports in Computational Chemistry, Vol. 4 by Ralph A. Wheeler, David C. Spellmeyer

By Ralph A. Wheeler, David C. Spellmeyer

Annual stories in Computational Chemistry is a brand new periodical supplying well timed and demanding experiences of vital subject matters in computational chemistry as utilized to all chemical disciplines. subject matters coated comprise quantum chemistry, molecular mechanics, strength fields, chemical schooling, and functions in educational and commercial settings. each one quantity is geared up into (thematic) sections with contributions written via specialists. targeting the newest literature and advances within the box, every one article covers a particular subject of value to computational chemists. Annual stories in Computational Chemistry is a "must" for researchers and scholars wishing to stick updated on present advancements in computational chemistry.

* wide insurance of computational chemistry and updated details
* subject matters lined contain bioinformatics, drug discovery, protein NMR, simulation methodologies, and purposes in educational and business settings
* each one bankruptcy reports the latest literature on a particular subject of curiosity to computational chemists

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CavBase [38], SURFACE [39], and SitesBase [40] are three examples. CavBase converts the portions of binding site residues exposed to solvent into sets of points defined by one of five pseudocenter types (aliphatic, donor, acceptor, donor/acceptor, and aromatic). For instance, a tyrosine is represented by an “aromatic” pseudocenter placed in the middle of the phenyl ring and a “donor/acceptor” pseudocenter placed at the oxygen of the hydroxyl. The constellation of pseudocenters representing a binding site is then compared to those of other binding sites using clique-detection algorithms that identify matching portions of the constellations.

Chem. 2005, 48, 4138–52. 8. , Hemmerle, H. Kinomicsstructural biology and chemogenomics of kinase inhibitors and targets. Biochim. Biophys. Acta 2004, 1697, 243–57. 9. M. Kinomics: Characterizing the therapeutically validated kinase space. Drug Discov. Today 2005, 10, 839–46. 10. M. Linear quantitative structure–activity relationships for the interaction of small molecules with human cytochrome P450 isoenzymes. Ann. Reports Comp. Chem. 2005, 1, 63–81. 11. R. Cytochrome P450 enzymes: Computational approaches to substrate prediction.

A variety of methods are available to cluster sequences and identify similarities starting from the multiple sequence alignment, with the most straightforward of these being pair-wise measurement of sequence identity or sequence similarity. Sequence identity is the percent of the residue positions that match, while sequence similarity involves a substitution matrix where amino acid residue similarity is taken into account. A more sophisticated approach to identify significantly related proteins is to infer a phylogenetic tree based on the multiple sequence alignment.

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