Motif-based searching

Gilbert, D., et ah, Motif-based searching in TOPS protein topology databases. Bioinformatics, 1999. 15(4) p. 317-26. 

An excellent example of motif based search strategies is found in the work of Dappen, Karfunkel and Leusen [18]. These scientists were interested in understanding how chiral separations take place and then to use that knowledge to design enhanced stationary phases. The authors first determined experimentally that the R enantiomer of anal el is bound more tightly to 2, a chiral stationary phase selector that is tethered to silica by the amino group. 

Thornton, J.M., Gardner, S.P. Protein motifs and data-base searching. Trends Biochem. Sci. 14 300-304, 1989. 

META-MEME [93-95] can be used to integrate motifs discovered by MEME, as well as information derived from sets of related sequences, into a single motif-based HMM. The latter can be used to search sequence databases for homologs. 

J. M. Thornton and S. P. Gardner, Trends Biochem. Sci., 14, 300 (1989). Protein Motifs and Data-Base Searching. 

Bucher, P., Karplus, K., Moeri, N., and Hofmann, K. (1996). A flexible motif search technique based on generalized profiles. Comput. Chem. 20, 3-23. 

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