Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

5.4K
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...
5.4K
Protein Folding01:25

Protein Folding

12.0K
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...
12.0K
Protein Folding01:22

Protein Folding

129.4K
Overview
129.4K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

12.0K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
12.0K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

4.2K
4.2K
Improving Translational Accuracy02:07

Improving Translational Accuracy

15.3K
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...
15.3K

You might also read

Related Articles

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

Sort by
Same author

Conserved enhancer association of piRNAs and the implication in germ cell fate surveillance.

Genome biology·2026
Same author

Functional cure for chronic hepatitis B on hepatocellular carcinoma prevention: Evidence and clinical implications.

iLIVER·2026
Same author

Diagnostic Accuracy of Urine Flow Cytometry (UF) in Urinary Tract Infection (UTI) Detection and Management: A Systematic Review and Meta-Analysis.

Diagnostics (Basel, Switzerland)·2026
Same author

Multimodal Integration of Ambulatory ECG and Clinical Features for Sudden Cardiac Death and Pump Failure Death Prediction<sup>★</sup>.

medRxiv : the preprint server for health sciences·2026
Same author

Ultrafast anisotropic exciton transport in phosphorene.

Nanoscale·2026
Same author

UDFStudio: A Unified Framework of Datasets, Benchmarks and Generative Models for Unsigned Distance Functions.

IEEE transactions on pattern analysis and machine intelligence·2026
Same journal

Region-aware bridge modeling enables interpretable mesoscale representation of spatial transcriptomic tissue sections.

Bioinformatics advances·2026
Same journal

Microbiome differential abundance methodologies to detect relevant taxa associated with chemotherapy toxicity rate in colorectal cancer.

Bioinformatics advances·2026
Same journal

maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation.

Bioinformatics advances·2026
Same journal

RAM-MSA: an anytime memory-bounded method for exact multiple sequence alignment using path finding.

Bioinformatics advances·2026
Same journal

Interpretable machine learning for low-sample multi-omics: a case study of ferret vaccine response.

Bioinformatics advances·2026
Same journal

DeepTaxa: a hybrid CNN-BERT framework for 16S rRNA taxonomic classification.

Bioinformatics advances·2026
See all related articles

Related Experiment Video

Updated: Mar 6, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.7K

LinearCDSfold: a tool for co-optimizing secondary structure stability and codon usage in coding sequence design.

Yu-Shen Liu1, Yan-Ru Ju1, Kai-Wei Chang1

  • 1Department of Computer Science, National Tsing Hua University, Hsinchu 30013, Taiwan.

Bioinformatics Advances
|March 5, 2026
PubMed
Summary
This summary is machine-generated.

LinearCDSfold now efficiently generates Pareto-optimal mRNA coding sequences (CDSs) for vaccine design. This tool optimizes both RNA secondary structure stability and codon usage, offering a faster alternative to existing methods.

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.8K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.2K

Related Experiment Videos

Last Updated: Mar 6, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.7K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.8K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.2K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Synthetic Biology

Background:

  • Designing mRNA coding sequences (CDSs) for vaccines requires optimizing RNA secondary structure stability (minimum free energy, MFE) and codon usage (codon adaptation index, CAI).
  • Existing tools often struggle to balance these competing objectives, necessitating methods for generating Pareto-optimal CDSs where neither objective can be improved without worsening the other.

Purpose of the Study:

  • To enhance the LinearCDSfold tool for automatic and efficient generation of Pareto-optimal CDSs.
  • To provide a superior alternative for co-optimizing MFE and CAI in mRNA vaccine design.

Main Methods:

  • Utilized dynamic programming and beam search techniques within the LinearCDSfold framework.
  • Extended LinearCDSfold to generate a set of Pareto-optimal CDSs, considering both MFE and CAI simultaneously.
  • Evaluated performance on nine diverse protein sequences.

Main Results:

  • The enhanced LinearCDSfold efficiently generates Pareto-optimal CDSs.
  • Performance was comparable to the existing tool DERNA in terms of Pareto-optimal set generation.
  • LinearCDSfold demonstrated substantially faster runtime compared to DERNA.

Conclusions:

  • LinearCDSfold is a powerful and efficient tool for generating Pareto-optimal CDSs for mRNA vaccine development.
  • The enhanced version offers a significant speed advantage, accelerating the design process.
  • This advancement facilitates the co-optimization of RNA structure and codon usage in synthetic biology applications.