Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.

by: M Zuker, P Stiegler

Nucleic Acids Res, Vol. 9, No. 1. (10 January 1981), pp. 133-148.

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Abstract

This paper presents a new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies. It is based on a dynamic programming algorithm from applied mathematics, and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature. Its power is demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1 heavy chain messenger RNA fragment. We go beyond the basic method to show how to incorporate additional information into the algorithm. This includes data on chemical reactivity and enzyme susceptibility. We illustrate this with the folding of two large fragments from the 16S ribosomal RNA of Escherichia coli.

@article{citeulike:118611, abstract = {This paper presents a new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies. It is based on a dynamic programming algorithm from applied mathematics, and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature. Its power is demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1 heavy chain messenger RNA fragment. We go beyond the basic method to show how to incorporate additional information into the algorithm. This includes data on chemical reactivity and enzyme susceptibility. We illustrate this with the folding of two large fragments from the 16S ribosomal RNA of Escherichia coli.}, author = {Zuker, M. and Stiegler, P. }, citeulike-article-id = {118611}, doi = {10.1093/nar/9.1.133}, issn = {0305-1048}, journal = {Nucleic Acids Res}, keywords = {ab-initio, biophysics, folding, rna}, month = {January}, number = {1}, pages = {133--148}, posted-at = {2006-03-18 20:59:28}, priority = {2}, title = {Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.}, url = {http://dx.doi.org/10.1093/nar/9.1.133}, volume = {9}, year = {1981} }

RIS record

TY - JOUR ID - citeulike:118611 L3 - citeulike-article-id:118611 TI - Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. JF - Nucleic Acids Res VL - 9 IS - 1 SP - 133 EP - 148 SN - 0305-1048 N2 - This paper presents a new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies. It is based on a dynamic programming algorithm from applied mathematics, and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature. Its power is demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1 heavy chain messenger RNA fragment. We go beyond the basic method to show how to incorporate additional information into the algorithm. This includes data on chemical reactivity and enzyme susceptibility. We illustrate this with the folding of two large fragments from the 16S ribosomal RNA of Escherichia coli. KW - ab-initio KW - biophysics KW - folding KW - rna AU - Zuker, M AU - Stiegler, P PY - 1981/01/10/ UR - http://dx.doi.org/10.1093/nar/9.1.133 ER -

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