Divide and Conquer Strategies for Protein Structure Prediction - Mathematical Approaches to Polymer Sequence Analysis and Related Problems - page 44

2.6 Conclusions

In this chapter, we presented two different aspects of the protein structure prediction
problem: the prediction of protein secondary structure, which is simpler in its for-
mulation than the protein folding problem and from which sequential annotations
can be derived, and the most demanding problem of residue contact prediction in
proteins. The first relevant message from our analysis of the current state-of-the-art
methods is that a key-role is played by evolutionary information. This knowledge,
which can be exploited by using different multiple sequence alignment methods, is
one of the major resources to identify relevant domains of the protein that are re-
lated to secondary structure elements or packing regions. A second relevant message
is that the most successful predictors are based on machine-learning tools, indicat-
ing that for the described tasks (at least up-to-now) bottom-up approaches compete
favorably with the methods that directly predict the 3D structure of the proteins.

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