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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...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Computing folding pathways between RNA secondary structures.

Ivan Dotu1, William A Lorenz, Pascal Van Hentenryck

  • 1Department of Computer Science, Brown University, PO Box 1910 Providence, RI 02912, USA.

Nucleic Acids Research
|January 2, 2010
PubMed
Summary
This summary is machine-generated.

We developed RNAtabupath, a novel algorithm for computing RNA folding pathways between two structures. This new method is significantly faster than existing tools, offering efficient analysis of RNA conformational changes.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Biophysics

Background:

  • RNA molecules fold into complex secondary structures essential for their function.
  • Predicting the dynamic pathway of RNA folding is crucial for understanding conformational changes.
  • Existing algorithms for computing folding pathways can be computationally intensive.

Purpose of the Study:

  • To introduce RNAtabupath, a new algorithm for calculating near-optimal RNA folding pathways.
  • To compare the performance of RNAtabupath against existing methods for pathway computation.
  • To provide a web server and associated resources for analyzing RNA folding pathways.

Main Methods:

  • Development of RNAtabupath, utilizing a tabu semi-greedy heuristic for combinatorial optimization.
  • Benchmarking RNAtabupath against other algorithms, including the barriers program from the Vienna RNA Package.
  • Application of the algorithm to experimentally determined structures of RNA conformational switches.

Main Results:

  • RNAtabupath computes RNA folding pathways significantly faster than the barriers program.
  • The algorithm successfully generates low-energy folding pathways between known RNA structures.
  • Demonstrated efficiency in analyzing pathways for conformational switches.

Conclusions:

  • RNAtabupath offers a computationally efficient approach to determining RNA folding pathways.
  • The tool facilitates the study of RNA dynamics and conformational transitions.
  • The RNApathfinder web server provides accessible resources for researchers.