The Ten Most Wanted Solutions in Protein Bioinformatics by Anna Tramontano PDF

By Anna Tramontano

ISBN-10: 1584884916

ISBN-13: 9781584884910

Using excessive velocity computational easy methods to extrapolate to the remainder of the protein universe, the data collected on a subset of examples, protein bioinformatics seeks to complete what was once very unlikely prior to its invention, particularly the task of services or practical hypotheses for all identified proteins.

The Ten such a lot sought after ideas in Protein Bioinformatics considers the 10 most vital difficulties occupying these seeking to determine the organic homes and useful roles of proteins.

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Extra resources for The Ten Most Wanted Solutions in Protein Bioinformatics

Example text

False positives are much more serious errors. They are related to the complexity of biological systems and cannot be solved by brute force. False positives not only can mislead biologists but also can, more importantly, cause error propagation in database functional assignment. Because of the speed at which new sequences are determined, the assignment of their function is mostly based on sequence similarity and, therefore, on the results of database searches, rather than on biochemical experiments.

Very long protein sequences are usually indicative of the presence of more than one domain, and we would like to search the database with each domain independently because they can be derived from different ancestral sequences. However, detecting domain boundaries in a protein sequence is not easy. Several methods are available that are described in Problem 2, but we should mention here that their reliability is not yet satisfactory. Reliability of Present Methods and Promising Avenues When discussing the reliability of bioinformatics tools, one must take into account the biological question that the tools are trying to address.

266, 383–402, 1996. R. Hidden Markov models, Curr. Opin. Struct. Biol. 6, 361–365, 1996. , and Chothia, C. Intermediate sequences increase the detection of homology between sequences, J. Mol. Biol. 273, 349–354, 1997. T. Coffee: a novel method for fast and accurate multiple sequence alignment, J. Mol. Biol. 302, 205–217, 2000. Problem 2 Predicting Protein Features from the Sequence Introduction to the Problem The pattern of secondary structure elements of a protein, the sites, if any, where it is posttranslationally modified, the cellular compartments where it resides, and many other functional features are specified by the amino acid sequence.

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The Ten Most Wanted Solutions in Protein Bioinformatics by Anna Tramontano


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