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Related Concept Videos

Protein Organization01:24

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 Organization01:13

Protein Organization

Overview
Protein Organization01:24

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 Organization01:13

Protein Organization

Overview
Conservation of Protein Domains Over Different Proteins02:26

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 form...
Protein and Protein Structure02:15

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 can...

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Related Experiment Video

Updated: May 11, 2026

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

Efficient Adaptation of Structure-Aware Protein Language Models for Diverse Protein Applications.

Duolin Wang1,2, Yichuan Zhang1,2, Yongfang Qin1,2

  • 1Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri.

Current Protocols
|May 9, 2026
PubMed
Summary

We developed structure-aware protein language models (PLMs) that integrate 3D structural data with sequence information. These models enhance protein prediction tasks by leveraging both sequence and structural features for improved performance.

Keywords:
protein analysesprotein language modelprotein predictionprotein sequenceprotein structure

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Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Machine Learning

Background:

  • Protein language models (PLMs) excel at sequence-based prediction but lack 3D structural insights.
  • Integrating 3D structural information is crucial for advancing protein prediction accuracy.

Purpose of the Study:

  • To develop novel structure-aware protein language models (S-PLMs) that incorporate 3D structural features.
  • To provide protocols for adapting S-PLMs for various protein applications and downstream analyses.

Main Methods:

  • Developed S-PLM1 using contact maps (Swin-Transformer) and S-PLM2 using backbone coordinates (GVP-based model).
  • Employed multi-view contrastive learning to align protein sequences and 3D structures.
  • Utilized AlphaFoldDB for paired sequence-structure data and designed efficient tuning strategies.

Main Results:

  • S-PLM1 and S-PLM2 effectively integrate sequence and structural information into a unified latent space.
  • Efficient tuning strategies optimize model performance with minimal computational cost.
  • Protocols enable generation of structure-aware representations and fine-tuning for diverse prediction tasks.

Conclusions:

  • Structure-aware PLMs significantly improve upon sequence-only models by incorporating 3D structural data.
  • Provided comprehensive protocols and code for practical application and customization of S-PLMs.
  • Facilitates structure-based downstream analyses and enhances protein understanding.