The prediction of a protein and nucleic acid structure: Problems and prospects (Q1061043)

We review some of the problems related to structure predictions: sequence homology searches, secondary structure prediction in RNAs, and regular structure prediction in proteins. The first two are mathematically well- defined problems, for it is not usually necessary to consider long-range interactions. The solution to a smaller segment is a part of the solution to the entire sequence. Thus, the problem can be solved by dynamic programming algorithms. The prediction of protein structures poses a more complex combinatorial problem, as illustrated in our statistical mechanical treatment. A promising approximation is to calculate locally optimal structures stabilized by relatively short-range interactions, and then to include longer-range effects as interactions between the locally optimal structures.