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...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Protein Organization

Protein Organization

You might also read

Related Articles

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

Sort by

Same author

Rational design of mechanically active RNAs: de novo engineering of functional exoribonuclease-resistant RNAs.

Nucleic acids research·2026

Same author

zelll: a fast, framework-free, and flexible implementation of the cell lists algorithm for the Rust programming language.

Bioinformatics advances·2026

Same author

Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques.

Nucleic acids research·2026

Same author

Dynamont: A comprehensive cross-species comparison of ONT segmentation tools.

GigaScience·2026

Same author

Nanopore sequencing enables novel detection of deuterium incorporation in DNA.

Computational and structural biotechnology journal·2025

Same author

Sequence Design for RNA-RNA Interactions.

Methods in molecular biology (Clifton, N.J.)·2024

Same journal

circ2DGNN: circRNA-Disease Association Prediction via Transformer-Based Graph Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

Hierarchical Hypergraph Learning in Association- Weighted Heterogeneous Network for miRNA- Disease Association Identification.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

Discriminative Domain Adaption Network for Simultaneously Removing Batch Effects and Annotating Cell Types in Single-Cell RNA-Seq.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

MLW-BFECF: A Multi-Weighted Dynamic Cascade Forest Based on Bilinear Feature Extraction for Predicting the Stage of Kidney Renal Clear Cell Carcinoma on Multi-Modal Gene Data.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

An End-to-End Knowledge Graph Fused Graph Neural Network for Accurate Protein-Protein Interactions Prediction.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Same journal

Generative Biomedical Event Extraction With Constrained Decoding Strategy.

IEEE/ACM transactions on computational biology and bioinformatics·2024

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 4, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Product Grammars for Alignment and Folding.

Christian Höner Zu Siederdissen, Ivo L Hofacker, Peter F Stadler

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|September 11, 2015

Summary

This summary is machine-generated.

We introduce a new algebraic theory for combining simple grammars into complex ones, enabling novel sequence alignment algorithms. This framework simplifies the construction and implementation of sophisticated bioinformatics tools.

More Related Videos

Folding and Characterization of a Bio-responsive Robot from DNA Origami

Folding and Characterization of a Bio-responsive Robot from DNA Origami

Published on: December 3, 2015

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

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

Published on: July 14, 2015

Related Experiment Videos

Last Updated: Apr 4, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Folding and Characterization of a Bio-responsive Robot from DNA Origami

Folding and Characterization of a Bio-responsive Robot from DNA Origami

Published on: December 3, 2015

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

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

Published on: July 14, 2015

Area of Science:

Bioinformatics
Theoretical Computer Science
Computational Biology

Background:

Sequence alignment is crucial in bioinformatics.
Existing methods struggle with complex, multi-sequence alignments.
Grammar-based approaches offer a structured way to define alignment problems.

Purpose of the Study:

To develop a theory of algebraic operations for grammars.
To construct complex alignment search spaces from simple grammars.
To implement a frameshift-aware DNA-protein alignment algorithm.

Main Methods:

Algebraic operations on linear and context-free grammars.
Composition of atomic grammars into multi-dimensional grammars.
Haskell domain-specific language embedding for grammar products.

Main Results:

A novel framework for algebraic grammar combination.
Explicit construction of complex alignment search spaces.
A frameshift-aware, semiglobal DNA-protein alignment algorithm.

Conclusions:

The algebraic grammar theory facilitates the creation of complex alignment algorithms.
The framework simplifies experimentation and implementation.
Direct accessibility via Haskell reduces implementation barriers.