Databases search procedures

Although the BLOSUM model is not explicitly evolutionary, the clumping procedure, which is required to construct a series of matrices, may be interpreted in evolutionary terms. The restriction of counts to conserved regions makes these matrices especially appropriate for database searching, where distant relationships are detected primarily because conserved positions are shared. 

Matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)-mass spectrometry (MS) is now routinely used in many laboratories for the rapid and sensitive identification of proteins by peptide mass fingerprinting (PMF). We describe a simple protocol that can be performed in a standard biochemistry laboratory, whereby proteins separated by one- or two-dimensional gel electrophoresis can be identified at femtomole levels. The procedure involves excision of the spot or band from the gel, washing and de-stain-ing, reduction and alkylation, in-gel trypsin digestion, MALDI-TOF MS of the tryptic peptides, and database searching of the PMF data. Up to 96 protein samples can easily be manually processed at one time by this method. 

The present book chapter presents an actual summary on the use of LC-MS-based procedures applied to mammalian samples for qualitative and quantitative analysis of tropane alkaloids (TA). Relevant literature obtained from PubMed database search and references cited therein is summarized and commented to provide an overview on various natural TA structures and their related pharmaceutical derivatives. A comprehensive unique set of TA was compiled that is categorized by diverse fields of analytical applications. 

Database search programs like FASTA [18] or BLAST [19] have been optimised to detect evolutionary relationships between proteins, and are readily adequate for template recognition and (multiple) sequence alignment in cases where the sequence identity is over 25-30% [20], The general procedure is to assume next that the backbone of the model is identical to the one of the template structure and add the side chains onto it [21], although some difficulties may arise with insertions, deletions and local low similarity. 

The pharmacophore model obtained by the mapping procedure allows 3-D database searching (Fig. 8). Database searching can identify actives in different chemotypes relative to those utilized for pharmacophore generation. This procedure is often termed as... 

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