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...

Conserved Binding Sites

Conserved Binding Sites

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...

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

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...

Multi-pass Transmembrane Proteins and β-barrels

Multi-pass Transmembrane Proteins and β-barrels

In multi-pass transmembrane proteins, the polypeptide chain crosses the membrane more than once. The transmembrane polypeptide chain either forms an α-helix or β-strand structure. α-Helix containing multi-pass transmembrane proteins are ubiquitous, whereas β-strand containing ones are mainly found in gram-negative bacteria, mitochondria, and chloroplasts.
α-Helix containing multi-pass transmembrane proteins
Multi-pass transmembrane proteins such as...

Protein Organization

Protein Organization

Protein and Protein Structure

Protein and Protein Structure

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...

You might also read

Related Articles

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

Sort by

Same author

Fermentative iron reduction by a psychrotolerant Clostridium-dominant consortium enriched from Antarctic penguin-impacted soils.

Communications biology·2026

Same author

Oliceridine versus sufentanil: a systematic review and meta-analysis of postoperative nausea and vomiting.

BMC anesthesiology·2026

Same author

Breaking the barrier: from biosynthetic inhibition to multidimensional modulation of the mycobacterial cell wall in tuberculosis therapy.

Frontiers in pharmacology·2026

Same author

ChSCL9 negatively regulates citric acid accumulation via repressing PH4-PH5 module in kumquat.

Plant physiology·2026

Same author

The chemistry of habitable oceans in the Solar system.

Nature communications·2026

Same author

Deep metagenomics uncovers functional adaptations and pathogenic risks in the gut microbiome of Antarctic fur seals (Arctocephalus gazella).

Environmental microbiome·2026

Same journal

Somatosensory cortex shapes perceptual decision bias via the superior colliculus.

Research square·2026

Same journal

Combinatorial Targeting of Avapritinib-Driven MAP Kinase Activation in High-Grade Glioma.

Research square·2026

Same journal

Supporting Implementation of the National Standards for Cancer Survivorship Care: Development of the Cancer Survivorship Maturity Model (CSMM).

Research square·2026

Same journal

Operationalizing a walking exercise prescription based on 6-minute walk test results.

Research square·2026

Same journal

Age but not sex modifies lymphoid immune responses in murine sepsis.

Research square·2026

Same journal

Indirect effect, through aspects of neighborhood affluence and racial/ethnic composition, of receiving a Section 8 voucher on the prevalence of psychiatric disorders among boys and girls in the Moving to Opportunity study.

Research square·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 11, 2025

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

Improving AlphaFold predicted contacts in alpha-helical transmembrane proteins structures using structural features.

Aman Sawhney¹, Jiefu Li², Li Liao¹

¹Department of Computer and Information Sciences, University of Delaware, Smith Hall, 18 Amstel Avenue, Newark, DE, 19716,United States.

Research Square

|November 14, 2023

Summary

This summary is machine-generated.

Leveraging known protein structures significantly improves residue contact map predictions, outperforming AlphaFold2 by utilizing features from atomic structures. This enhances accuracy for predicting protein structure and function.

Keywords:

Alpha helix Alphafold Contact map prediction Machine learning Protein structure Protein structure modeling Transmembrane proteins

More Related Videos

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

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

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

Published on: July 25, 2013

Related Experiment Videos

Last Updated: Jul 11, 2025

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

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

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

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

Published on: July 25, 2013

Area of Science:

Structural biology
Computational biology
Bioinformatics

Background:

Residue contact maps are 2-D representations of 3-D protein structures, crucial for structural modeling and understanding protein function.
Current methods primarily use sequence-based features for contact map prediction.
Known protein structures offer valuable information for improving predictions of unknown structures, especially when approximate models like AlphaFold2 are available.

Conclusions:

Knowledge from experimentally determined structures can substantially enhance contact predictions derived from AlphaFold2 models.
The proposed feature-based method significantly outperforms existing approaches for residue contact prediction.
This approach offers a more accurate way to analyze protein structures and functions using predicted models.