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Related Concept Videos

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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Protein Folding01:25

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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
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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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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Conservation of Protein Domains Over Different Proteins02:26

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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.
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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.
A protein's shape is critical to its function. For example, an enzyme...
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Updated: Jul 11, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
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AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences.

Mihaly Varadi1, Damian Bertoni1, Paulyna Magana1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.

Nucleic Acids Research
|November 7, 2023
PubMed
Summary
This summary is machine-generated.

The AlphaFold Database now provides over 214 million predicted protein structures, significantly expanding structural biology resources. Enhancements include new datasets, improved data access, and upgraded visualization tools.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Artificial Intelligence in Biology

Background:

  • The AlphaFold Database (AlphaFold DB) has revolutionized structural biology with AI-driven protein structure predictions.
  • Initial release in 2021 contained 300,000 structures; now exceeds 214 million.
  • AlphaFold DB predictions are integrated into major biological databases like UniProt and PDB.

Purpose of the Study:

  • To detail the expansion and enhancements of the AlphaFold Database.
  • To describe new data releases, access methods, and improved services.
  • To highlight the growing impact of AI-predicted protein structures.

Main Methods:

  • Archiving of successive AlphaFold DB releases, including model organisms and global health proteomes.
  • Integration of curated protein datasets and Swiss-Prot.
  • Development of diverse data access mechanisms: FTP, Google Cloud Public Datasets, and programmatic endpoints.

Main Results:

  • Expansion to over 214 million predicted protein structures.
  • Inclusion of diverse datasets such as model organisms, global health proteomes, and Swiss-Prot.
  • Enhanced data access and improved user tools, including the Predicted Aligned Error viewer and 3D viewer.

Conclusions:

  • The AlphaFold Database has become an indispensable resource for structural biology research.
  • Continuous updates and service improvements enhance data accessibility and utility.
  • The database demonstrates the transformative power of AI in biological discovery.