By Des Higgins, Willie Taylor

This quantity covers useful very important themes within the research of protein sequences and buildings. It comprises evaluating amino acid sequences to constructions evaluating buildings to one another, looking info on whole protein households in addition to looking out with unmarried sequences, how one can use the net and the way to establish and use the SRS molecular biology database administration approach. eventually, there are chapters on a number of series alignment and protein secondary constitution prediction. This ebook can be precious to occasional clients of those suggestions in addition to skilled pros or researchers.

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Additional info for Bioinformatics: Sequence, Structure and Databanks: A Practical Approach

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Mol. , 244, 332. 18. Orengo, C. , Jones, D. , and Thornton, J. M. (1994). Protein superfamilies and domain superfolds. Nature, 372, 631. 19. Kraulis, P. J. (1991). Molscript—a program to produce both detailed and schematic plots of protein structures. J . Appl. , 24, 946. 20 Jones, D. , and Thornton, J. M. (1996). Potential energy functions for threading. Curr. Opin. Struct. , 6, 210. 13 This page intentionally left blank Chapter 2 Comparison of protein three-dimensional structures Mark S. Johnson and Jukka V.

RMSD is not a good way to evaluate models of this quality as very large shifts in the alignment produce virtually random RMSD values. 2 Post-processing threading results Perhaps one of the most significant observations that came from the CASP2 prediction experiment was that a great deal of success in fold recognition can be achieved purely from a deep background knowledge of protein structure and function relationships. Alexey Murzin (one of the authors of the SCOP protein structure classification scheme) identified a number of key evolutionary clues which led him to correctly assign membership of some of the target proteins to known superfamilies (16).

Frequently, however, global comparisons are made between proteins where the best-matched positions are not obvious in advance. In the case of similar protein structures, the requirement of an initial set of matches to seed the comparison is inconvenient at best, requires the preanalysis of the proteins involved, and in the case of more dissimilar proteins, may be difficult to define. Additionally, we have often observed that when part of the answer is specified at the beginning of the comparison, then the final solution can be prejudiced to give a final result that is not necessarily the optimal one: The comparison was locked into a set of possible solutions by the information supplied to seed the procedure.

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