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Related Concept Videos

Protein Organization01:24

Protein Organization

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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....
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Protein Folding01:22

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Overview
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Protein Folding01:25

Protein Folding

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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
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Protein and Protein Structure02:15

Protein and Protein Structure

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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.
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Protein Folding Quality Check in the RER01:29

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ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
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Protein Families02:47

Protein Families

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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...
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Updated: Jan 10, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Rapid and Accurate Protein Structure Database Search Using Inverse Folding Model and Contrastive Learning.

Qiuyi Lyu1, Hong Wei2, Shuaishuai Chen3

  • 1MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China.

Journal of Chemical Information and Modeling
|November 26, 2025
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We developed mTM-align2, a fast and accurate protein structure search method. It uses advanced embeddings and alignment to quickly find similar protein structures in large databases.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • Protein structure database searching is increasingly difficult due to the vast number of available structures.
  • Existing methods struggle with speed and accuracy for large-scale protein structure comparisons.

Purpose of the Study:

  • To introduce mTM-align2, a novel two-step approach for rapid and accurate protein structure database searching.
  • To provide a computationally efficient tool for identifying structurally similar proteins.

Main Methods:

  • Utilizing a pretrained inverse folding model (ESM-IF) and 3D Zernike polynomials to generate protein structure embeddings.
  • Optimizing embeddings via a contrastive learning network trained on millions of structure pairs.
  • Employing a rapid structure alignment program for refining top candidate structures.

Main Results:

  • mTM-align2 achieves competitive performance against leading methods in protein structure database search.
  • The method performs monomeric structure searches in seconds with over 90% precision for top 10 hits.
  • Embeddings generated by mTM-align2 are structurally informed, capturing global protein features.

Conclusions:

  • mTM-align2 offers a significant advancement in rapid and accurate protein structure database searching.
  • The developed embeddings effectively represent global structural characteristics of proteins.
  • A web server is available for accessing the mTM-align2 tool.