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Related Concept Videos

RNA Structure01:19

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Related Experiment Video

Updated: Jun 20, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
13:42

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Improved RNA secondary structure prediction by maximizing expected pair accuracy.

Zhi John Lu1, Jason W Gloor, David H Mathews

  • 1Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA.

RNA (New York, N.Y.)
|August 26, 2009
PubMed
Summary

MaxExpect maximizes expected base-pair accuracy for RNA secondary structure prediction, outperforming traditional free energy minimization. This new method improves prediction accuracy for RNA structures.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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Published on: March 12, 2012

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Free energy minimization is a long-standing standard for RNA secondary structure prediction.
  • This method relies on empirical nearest-neighbor thermodynamic parameters.
  • Limitations exist in accurately predicting complex RNA structures.

Purpose of the Study:

  • Introduce MaxExpect, a novel program for RNA secondary structure prediction.
  • To improve upon the accuracy of minimum free energy (MFE) approaches.
  • To provide alternative structural hypotheses beyond the optimal structure.

Main Methods:

  • Utilizes partition function calculations with nearest-neighbor parameters.
  • Predicts base-pair probabilities and nucleotide single-stranded probabilities.
  • Maximizes expected base-pair accuracy, unlike MFE methods.

Main Results:

  • MaxExpect structures demonstrate higher average accuracy than MFE structures.
  • Achieved improved positive predictive value (PPV) from 66% to 68% at 73% sensitivity.
  • Demonstrated ability to favor sensitivity or PPV by adjusting prediction parameters.

Conclusions:

  • MaxExpect offers a more accurate RNA secondary structure prediction method.
  • The approach provides valuable suboptimal structures as alternative hypotheses.
  • This method advances RNA structure prediction beyond traditional MFE.