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

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...

You might also read

Related Articles

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

Sort by

Same author

Metabologenomic profiling of the endemic Australian fungus <i>Aspergillus luteorubrus</i>.

Mycology·2026

Same author

PMGen: from peptide-MHC structure prediction to peptide generation.

Bioinformatics (Oxford, England)·2026

Same author

Structural motif search across the protein universe with Folddisco.

Nature biotechnology·2026

Same author

Mapping interactions between disordered regions reveals promiscuity in biomolecular condensate formation.

Nature communications·2026

Same author

A novel method to select Reference Proteomes in UniProt.

bioRxiv : the preprint server for biology·2026

Same author

Simple and Thorough Detection of Related Sequences with Position-Varying Probabilities of Substitutions, Insertions, and Deletions.

Journal of computational biology : a journal of computational molecular cell biology·2026

Same journal

RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.

Nature methods·2026

Same journal

Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.

Nature methods·2026

Same journal

EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control.

Nature methods·2026

Same journal

Cloud-based microscope enables live neuroimaging for 24 h and beyond with worldwide access.

Nature methods·2026

Same journal

Deep molecular profiling in three dimensions.

Nature methods·2026

Same journal

3D pathology-guided microdissection.

Nature methods·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 29, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Rapid and sensitive protein complex alignment with Foldseek-Multimer.

Woosub Kim^1,2, Milot Mirdita², Eli Levy Karin³

¹Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.

|February 5, 2025

Summary

This summary is machine-generated.

Computational structure prediction is rapidly expanding protein complex data. Foldseek-Multimer accelerates the alignment of these protein complexes, enabling faster scientific discovery.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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: May 29, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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:

Structural bioinformatics
Computational biology
Biochemistry

Background:

Computational structure prediction methods are generating vast amounts of protein complex data.
Aligning these protein complexes is crucial for deriving biological insights but is computationally intensive.
Existing alignment methods face scalability challenges with the growing size of structural databases.

Purpose of the Study:

To develop a computationally efficient method for aligning protein complexes.
To enable the comparison of billions of protein complex structures within a practical timeframe.
To facilitate the discovery of novel biological functions and interactions from predicted structures.

Main Methods:

Foldseek-Multimer identifies compatible chain-to-chain alignments by clustering superposition vectors.
The method leverages efficient clustering algorithms for rapid identification of related structures.
Complex alignments are computed based on these pre-identified compatible chain alignments.

Main Results:

Foldseek-Multimer achieves alignment speeds 3-4 orders of magnitude faster than current gold-standard methods.
The software can compare billions of protein complex pairs in approximately 11 hours.
The alignments generated by Foldseek-Multimer are comparable in quality to existing methods.

Conclusions:

Foldseek-Multimer significantly overcomes the computational bottleneck in protein complex alignment.
The speed and scalability of Foldseek-Multimer democratize the analysis of large structural datasets.
This advancement will accelerate discoveries in structural biology and drug development.