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Related Concept Videos

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...
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...
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...
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Articles linked to this work by shared authors, journal, and citation graph.

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Same author

GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization.

Bioinformatics (Oxford, England)·2017
Same author

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

PloS one·2015
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Analyzing and Building Nucleic Acid Structures with 3DNA
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GARN3: A coarse-grained helix centered technique for RNA 3D structures prediction.

Jhonatan Silva1, Johanne Cohen2, Daniel Cordeiro1

  • 1Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, São Paulo, Brazil.

Plos One
|June 22, 2026
PubMed
Summary

GARN3 enhances RNA 3D structure prediction by adding pseudoatoms and machine learning to the GARN framework. This improves model granularity and accuracy for RNA molecules, especially large ones.

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RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Predicting three-dimensional (3D) RNA structures is crucial and has advanced with AI.
  • Existing methods like the Game Algorithms for RNa 3D sampling (GARN) framework show promise but require refinement.
  • Further improvements in RNA 3D models can be achieved by incorporating pseudoatoms and advanced scoring functions.

Purpose of the Study:

  • To introduce GARN3, an enhanced version of the GARN framework for RNA 3D structure prediction.
  • To improve the granularity and accuracy of predicted RNA 3D models.
  • To integrate a machine learning component for estimating interaction distances.

Main Methods:

  • GARN3 extends GARN2 by adding pseudoatoms along helices to refine 3D models.
  • A machine learning component is incorporated into the scoring function to estimate interaction distances.
  • Experimental validation using RMSD and TM-score evaluations against existing RNA 3D structure prediction methods.

Main Results:

  • GARN3 achieved Root Mean Square Deviation (RMSD) values comparable to or better than existing methods.
  • TM-score evaluations demonstrated consistent global structural accuracy across multiple RNA molecules.
  • GARN3 improved upon previous GARN versions, particularly for large RNA structures, offering finer coarse-grained representations.

Conclusions:

  • GARN3 represents a significant advancement in RNA 3D structure prediction.
  • The method provides improved granularity and accuracy, especially for large RNA molecules.
  • The GARN3 implementation is publicly available for further research and application.