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

The prediction of a protein and nucleic acid structure: Problems and prospects Recent advances in DNA and protein-sequencing technologies have made an increasing number of primary structures available for theoretical investigations. The prediction of a higher-order protein, and nucleic acid structure in particular, is an area where computational approaches will be able to complement the lack of experimental observations. 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Acta Applicandae Mathematicae Springer Journals

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

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References (4)

Publisher
Springer Journals
Copyright
Copyright
Subject
Mathematics; Computational Mathematics and Numerical Analysis; Applications of Mathematics; Partial Differential Equations; Probability Theory and Stochastic Processes; Calculus of Variations and Optimal Control; Optimization
ISSN
0167-8019
eISSN
1572-9036
DOI
10.1007/BF00052458
Publisher site
See Article on Publisher Site

Abstract

Recent advances in DNA and protein-sequencing technologies have made an increasing number of primary structures available for theoretical investigations. The prediction of a higher-order protein, and nucleic acid structure in particular, is an area where computational approaches will be able to complement the lack of experimental observations. 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.

Journal

Acta Applicandae MathematicaeSpringer Journals

Published: May 6, 2004

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