PMID: 6163133Jan 10, 1981Paper

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

Nucleic Acids Research
M Zuker, P Stiegler

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.

References

Sep 1, 1978·Nucleic Acids Research·G M StudnickaW A Salser
Jul 25, 1979·Nucleic Acids Research·J RogersW Salser
Jan 1, 1978·Cold Spring Harbor Symposia on Quantitative Biology·W Salser
Apr 15, 1976·European Journal of Biochemistry·J RinkeR Brimacombe
Jun 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·J M Pipas, J E McMahon
Nov 14, 1973·Nature: New Biology·I TinocoJ Bralla
Feb 5, 1973·Journal of Molecular Biology·O C UhlenbeckI Tinoco
Feb 5, 1973·Journal of Molecular Biology·J Gralla, D M Crothers
Aug 5, 1973·Journal of Molecular Biology·J Gralla, D M Crothers
Apr 9, 1971·Nature·I TinocoM D Levine
Feb 1, 1980·European Journal of Biochemistry·C EhresmannR A Garrett

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Citations

Apr 1, 1999·Biotechnology and Bioengineering·B T KohM G Yap
Nov 26, 2002·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Walter Fontana
Sep 1, 1993·Biopolymers·W FontanaP Schuster
Dec 1, 1990·Journal of Cellular Physiology·M H CorjayG K Owens
Jan 9, 2001·Bulletin of Mathematical Biology·C ReidysP Schuster
Jan 1, 1991·Plant Molecular Biology·E J DavidowitzN Lang-Unnasch
May 1, 1994·Plant Molecular Biology·S J TebbuttD M Lonsdale
Oct 1, 1993·Plant Molecular Biology·S J Tebbutt, D M Lonsdale
Oct 1, 1996·Plant Molecular Biology·P KlaffG Steger
Jan 1, 1993·Plant Molecular Biology·D LeaderJ W Brown
Sep 1, 1991·Plant Molecular Biology·M J SpenceP J Lammers
Nov 1, 1991·Molecular & General Genetics : MGG·M Ohman, E G Wagner
Dec 1, 1987·Molecular & General Genetics : MGG·J C Alonso, R H Tailor
Dec 1, 1987·Molecular & General Genetics : MGG·J E CroftP L Bergquist
Sep 1, 1987·Molecular & General Genetics : MGG·J Colasanti, D T Denhardt
Feb 1, 1988·Molecular & General Genetics : MGG·J MorlonC Lazdunski
Aug 1, 1989·Molecular & General Genetics : MGG·E L de HostosA R Grossman
Apr 1, 1989·Molecular & General Genetics : MGG·M N HayashiM Hayashi
May 1, 1988·Molecular & General Genetics : MGG·R A Kelln, J Neuhard
Nov 1, 1987·Molecular & General Genetics : MGG·K R Kearney, M Nomura
Jun 1, 1995·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Z PausovaG N Hendy
Oct 1, 1989·Die Naturwissenschaften·M D Purugganan
Jan 1, 1995·Archives of Dermatological Research·H NäherP Nickel

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