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Utilizing high speed computational methods to extrapolate to the rest of the protein universe, the knowledge accumulated on a subset of examples, protein bioinformatics seeks to accomplish what was impossible before its invention, namely the assignment of functions or functional hypotheses for all known proteins.

The Ten Most Wanted Solutions in Protein Bioinformatics considers the ten most significant problems occupying those looking to identify the biological properties and functional roles of proteins.

- Problem One considers the challenge involved with detecting the existence of an evolutionary relationship between proteins.
- Two and Three studies the detection of local similarities between protein sequences and analysis in order to determine functional assignment.
- Four, Five, and Six look at how the knowledge of the three-dimensional structures of proteins can be experimentally determined or inferred, and then exploited to understand the role of a protein.
- Seven and Eight explore how proteins interact with each other and with ligands, both physically and logically.
- Nine moves us out of the realm of observation to discuss the possibility of designing completely new proteins tailored to specific tasks.
- And lastly, Problem Ten considers ways to modify the functional properties of proteins.

After summarizing each problem, the author looks at and evaluates the current approaches being utilized, before going on to consider some potential approaches.