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 Organization

Protein Organization

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....

Protein and Protein Structures

Protein and Protein Structures

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...

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...

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...

RNA Structure

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...

You might also read

Related Articles

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

Sort by

Same author

Protein language models for structural biology.

Nature computational science·2026

Same author

mTM-align2: A Server for Real-time Protein Structure Database Search and Alignment.

Genomics, proteomics & bioinformatics·2026

Same author

The trRosettaRNA server for RNA structure prediction.

Nature protocols·2026

Same author

Hybrid deep learning with protein language models and dual-path architecture for predicting IDP functions.

Briefings in bioinformatics·2026

Same author

Generating Dynamic Structures Through Physics-Based Sampling of Predicted Inter-Residue Geometries.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026

Same author

Quality assessment of RNA 3D structure models using deep learning and intermediate 2D maps.

Communications biology·2026

Same journal

Gaining biological insights through supervised data visualization.

Nature computational science·2026

Same journal

The inequalities of GPU access.

Nature computational science·2026

Same journal

Social technologies need societal alignment.

Nature computational science·2026

Same journal

The Quantum Optimization Benchmarking Library.

Nature computational science·2026

Same journal

Setting benchmarks for practical quantum utility of combinatorial optimization.

Nature computational science·2026

Same journal

Evidence of scaling advantage on an NP-complete problem with enhanced quantum solvers.

Nature computational science·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 6, 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

Single-sequence protein structure prediction using supervised transformer protein language models.

Wenkai Wang¹, Zhenling Peng², Jianyi Yang³

¹School of Mathematical Sciences, Nankai University, Tianjin, China.

Nature Computational Science

|January 4, 2024

Summary

This summary is machine-generated.

trRosettaX-Single is a new algorithm for protein structure prediction from a single sequence. It is faster and uses fewer resources than AlphaFold2, showing promise for protein design and mutation analysis.

More Related Videos

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

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: Jul 6, 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

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

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:

Computational biology
Structural biology
Bioinformatics

Background:

Protein structure prediction is crucial for understanding protein function.
Deep learning methods like AlphaFold2 have advanced prediction but struggle with single-sequence inputs.
Accurate prediction for orphan and designed proteins remains a challenge.

Purpose of the Study:

To develop an automated algorithm for single-sequence protein structure prediction.
To improve the efficiency and resource utilization of protein structure prediction.
To explore applications in protein design and missense mutation analysis.

Main Methods:

Incorporated sequence embeddings from a supervised transformer protein language model.
Utilized a multi-scale network enhanced by knowledge distillation for 2D geometry prediction.
Reconstructed 3D structures using energy minimization.
Benchmarked against AlphaFold2 and RoseTTAFold.

Main Results:

trRosettaX-Single outperforms AlphaFold2 and RoseTTAFold on orphan proteins.
Achieved an average template modeling score (TM-score) of 0.79 on human-designed proteins.
The pipeline is 2x faster than AlphaFold2, using <10% of computing resources.
Generated high-confidence models for 2,000 designed proteins and demonstrated missense mutation analysis.

Conclusions:

trRosettaX-Single offers an efficient and effective approach for single-sequence protein structure prediction.
The algorithm shows significant potential for applications in protein design and related studies.
It provides a valuable tool for analyzing mutations and understanding protein behavior.