Amino acids database searching performance

The generation of loops is necessary because disconnected regions are often separated by a section where a few amino acids have been inserted or omitted. These are often extra loops that can be determined by several methods. One method is to perform a database search to find a similar loop and then use its geometric structure. Often, other conformation search methods are used. Manual structure building may be necessary in order to find a conformation that connects the segments. Visual inspection of the result is recommended in any case. 

Rather than using an amino acid sequence to search SWISS-PROT, AACompI-dent of ExPASy Proteomic tools (http //www.expasy.ch/tools/) uses the amino acid composition of an unknown protein to identify known proteins of the same composition. The program requires the desired amino acid composition, the pi and molecular weight of the protein (if known), the appropriate taxonomic class, and any special keywords. The user must select from one of six amino acid constellations that influence how the analysis is performed. For each sequence in the database, the algorithm computes a score based on the difference in compositions between the sequence and the query composition. The results, returned by e-mail, are organized as three ranked lists. Because the computed scores are a measure of difference, a score of zero implies that there is exact correspondence between the query compo-... 

Perform a similarity search of PIR database for a protein with the following amino acid sequence ... 

Figure 12.9. Protein structure prediction with PHD. The amino acid sequence of chicken lysozyme precursor (147 amino acids) is submitted to PredictProtein server for PHD structure predictions. The returned e-mail reports protein class based on secondary structures, predicted secondary structure composition (%H, %E, and %L), residue composition, data interpretation, and predicted data in two levels (brief and normal of which the normal is shown). Search for the database can be performed by making choice(s) from the list(s) of pop-up box(es).

To search amino acid sequence against the BLOCKS database at http // www.blocks.fhcrc.org/, select Block Searcher to open the search form. Choose the options, paste the query sequence, and click the Perform Search button. The search returns lists of matched blocks (I.D. descriptions, number of blocks, and combined E values), locations (amino acid positions of individual blocks and its E value), and pairwise alignment of the blocks with the matched query sequences (Figure 12.17). 

AACompSim, a variant of AACompIdent, performs a similar type of analysis, but, rather than using an experimentally derived amino acid composition as the basis for searches, the sequence of a SWISS-PROT protein is used instead (Wilkins et al., 1996). A theoretical pl and molecular weight are computed before computation of the difference scores using Compute pl/MW (see below). It has been documented that amino acid composition across species boundaries is well conserved (Cordwell et al., 1995) and that, by considering amino acid composition, investigators can detect weak similarities between proteins whose sequence identity falls below 25% (Ho-bohm and Sander, 1995). Thus the consideration of composition in addition to the ability to perform traditional database searches may provide additional insight into the relationships between proteins. 

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