Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein Folding

Protein Folding

Protein Folding

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...

Protein Folding

Protein Folding

Protein Folding Quality Check in the RER

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

RNA Structure

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 Structure

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...

You might also read

Related Articles

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

Sort by

Same author

DNAzyme based three-way junction assay for antibody-free detection of locus-specific N<sup>6</sup>-methyladenosine modifications.

Biosensors & bioelectronics·2021

Same author

Proximity ligation assay mediated rolling circle amplification strategy for in situ amplified imaging of glycosylated PD-L1.

Analytical and bioanalytical chemistry·2021

Same author

Dihydroartemisinin Induces O-GlcNAcylation and Improves Cognitive Function in a Mouse Model of Tauopathy.

Journal of Alzheimer's disease : JAD·2021

Same author

SnRK1 stimulates the histone H3K27me3 demethylase JMJ705 to regulate a transcriptional switch to control energy homeostasis.

The Plant cell·2021

Same author

Intratumoral injection of caerin 1.1 and 1.9 peptides increases the efficacy of vaccinated TC-1 tumor-bearing mice with PD-1 blockade by modulating macrophage heterogeneity and the activation of CD8<sup>+</sup> T cells in the tumor microenvironment.

Clinical & translational immunology·2021

Same author

Tilting Behavior of Lamellar Ice Tip during Unidirectional Freezing of Aqueous Solutions.

Langmuir : the ACS journal of surfaces and colloids·2021

Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026

Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026

Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026

Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026

Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026

Same journal

Benchmarking DNA barcode decoding strategies under high error rates.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 26, 2026

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Multicore and GPU algorithms for Nussinov RNA folding.

Junjie Li, Sanjay Ranka, Sartaj Sahni

BMC Bioinformatics

|August 2, 2014

Summary

This summary is machine-generated.

We developed faster RNA folding algorithms using Nussinov's method. Our cache-efficient, multicore, and GPU approaches significantly accelerate RNA secondary structure prediction.

More Related Videos

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Published on: February 27, 2026

Related Experiment Videos

Last Updated: Apr 26, 2026

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae

Published on: February 27, 2026

Area of Science:

Computational Biology
Bioinformatics
Molecular Biology

Background:

RNA secondary structure forms through hydrogen bonds between RNA segments.
Predicting RNA secondary structure is crucial for understanding RNA function.
RNA folding algorithms are computational methods for structure prediction.

Purpose of the Study:

To develop optimized algorithms for RNA folding using Nussinov's algorithm.
To improve the efficiency of RNA secondary structure prediction on modern hardware.

Main Methods:

Developed cache-efficient algorithms for single-core processors.
Implemented multicore algorithms leveraging parallel processing.
Created GPU-accelerated algorithms for high-performance computing.

Main Results:

Cache-efficient algorithm achieved 1.6–3.0x speedup over naive code.
Multicore algorithm showed 7.5–14.0x speedup on a 6-core CPU.
GPU algorithm provided up to 1582x speedup versus naive code and 5.1–11.2x over prior GPU methods.

Conclusions:

Optimized algorithms offer substantial performance improvements for RNA folding.
Cache efficiency, multicore, and GPU approaches enhance prediction speed.
The developed GPU algorithm represents a significant advancement in computational RNA folding.