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 Folding01:22

Protein Folding

117.2K
Overview
117.2K
Protein Organization01:24

Protein Organization

6.2K
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....
6.2K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.8K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.8K
Protein and Protein Structure02:15

Protein and Protein Structure

78.1K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
78.1K
Protein and Protein Structures02:15

Protein and Protein Structures

10.3K
10.3K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K

You might also read

Related Articles

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

Sort by
Same author

LetA defines a structurally distinct transporter family.

Nature·2026
Same author

Predicting protein-protein interactions in the human proteome.

Science (New York, N.Y.)·2025
Same author

Inhibition of FAM19A5 reverses synaptic loss and cognitive decline in mouse models of Alzheimer's disease.

Alzheimer's research & therapy·2025
Same author

LetA defines a structurally distinct transporter family involved in lipid trafficking.

bioRxiv : the preprint server for biology·2025
Same author

Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm.

Nature communications·2025
Same author

Deep learning methods for proteome-scale interaction prediction.

Current opinion in structural biology·2025
Same journal

Metabolic disruptions through a three-dimensional genomic lens.

Current opinion in structural biology·2026
Same journal

Collective variable design for biomolecular conformational dynamics.

Current opinion in structural biology·2026
Same journal

Polymer scaling in protein crowding: From dilute coils to semidilute meshes.

Current opinion in structural biology·2026
Same journal

Tuning the physicochemical properties of rationally designed protein-based biomolecular condensates.

Current opinion in structural biology·2026
Same journal

Editorial overview: Folding, binding and protein design.

Current opinion in structural biology·2026
Same journal

Macromolecular crowding reshapes the conformational landscapes of intrinsically disordered proteins: mechanisms, cellular contexts, and functional consequences.

Current opinion in structural biology·2026
See all related articles

Related Experiment Video

Updated: May 30, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.5K

Advancing protein structure prediction beyond AlphaFold2.

Sanggeun Park1, Sojung Myung2, Minkyung Baek1

  • 1Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.

Current Opinion in Structural Biology
|January 25, 2025
PubMed
Summary
This summary is machine-generated.

Accurate protein structure prediction is vital. This review explores enhancing AlphaFold2 using advanced sequence searches and AI, aiming for better predictions across diverse biological systems.

More Related Videos

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

17.0K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.4K

Related Experiment Videos

Last Updated: May 30, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.5K
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

17.0K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.4K

Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • Accurate protein structure prediction is crucial for understanding biological functions.
  • AlphaFold2 (AF2) significantly advanced prediction accuracy in 2021.
  • Challenges persist for proteins with limited evolutionary data or complex interactions.

Purpose of the Study:

  • To review methods for enhancing AlphaFold2 performance.
  • To explore alternative approaches for protein structure prediction.
  • To identify future directions for improving prediction accuracy and scope.

Main Methods:

  • Advanced sequence search techniques.
  • Integration of protein language models (PLMs).
  • Frameworks incorporating diverse biomolecular interactions.

Main Results:

  • Enhanced sequence searches improve AF2 accuracy for challenging proteins.
  • PLMs offer complementary predictive power.
  • Integrating multiple data types yields more robust predictions.

Conclusions:

  • Future protein structure prediction requires models grounded in physicochemical principles.
  • Enhanced AI and data integration will broaden prediction applicability.
  • Continued innovation is key for comprehensive biological system modeling.