A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation
نویسندگان
چکیده
منابع مشابه
A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation
Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction algorithms are to changes in these parameters. We found already that for changes corresponding to the actual experimental error to which these parameters have been...
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We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large enough loop costs the model exhibits a thermal denaturation transition which we analyze in terms of the radius of gyration. We point out an inconsistency in the ...
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Two different dynamical-parameter algortihms are discussed, simulated tempering and the multisequence method. Using simulated tempering, the folding properties of 300 random sequences in a simple off-lattice model with only two amino-acid types, hydrophobic and hydrophilic, are investigated. A careful statistical analysis shows that the hydrophobic monomers are anticorrelated along the chains f...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2005
ISSN: 1362-4962
DOI: 10.1093/nar/gkh983