Bioinformatics homologies

In summary, it is reasonable to conclude that bioinformatic analysis of structural similarities to, or of sequence homology with, known protein allergens, and evaluation of stability with SGF, can both contribute, if interpreted cautiously, to an overall assessment of sensitizing hazard. However, these analyses, neither alone nor in combination, provide a definitive answer regarding allergenic potential, and for this reason there has been interest in exploring a more holistic approach (and more definitive assessment) that may be provided by suitable animal models. 

For a reference supporting the importance of Arg358 and Phe357 for DPP-4 selectivity, see Rummy, C. and Metz, G. (2007) Homology models of dipeptidyl peptidases 8 and 9 with a focus on lop predictions near the active site. Proteins Structure, Function, and Bioinformatics, 66, 160-171. 

Henikoff, S., and Henikoff, J. G. (2000). Protein family-based methods for homology detection and analysis. In Bioinformatics, A Practical Approach. (D. Higgins, and W. Taylor, eds.), IRL Press, (In press). 

If PMF and sequence homology searches fail using available protein and EST databases, mass spectrum data can, in principle, be used to search genome databases (GenBank http //www.ncbi.nlm.nih.gov/). However, only a small percentage of large genomic sequences code for proteins such that bioinformatics still needs to accurately define exon-intron structures (Andersen and Mann, 2000). 

Muller T, Rahmann S, Rehmsmeier M. Nonmmetric score matrices and the detection of homologous transmembrane proteins. Bioinformatics 2001 17(suppl 1) S182-S189. 

Korf I, Flicek P, Duan D, Brent MR. Integrating genomic homology into gene structure prediction. Bioinformatics 2001 17(suppl 1) S140—S148. 

Arnold K, Bordoli L, Kopp J et al (2006) The SWISS-MODEL workspace a web-based environment for protein structure homology modelling. Bioinformatics 22 195-201... 

Sujatha S, Balaji S, Srinivasan N (2001) PALI a database of alignments and phylogeny of homologous protein structures. Bioinformatics 17 375-376... 

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