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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 Organization

Protein Organization

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...

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...

Protein Folding

Protein Folding

Protein and Protein Structures

Protein and Protein Structures

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Related Experiment Video

Updated: Jan 6, 2026

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

AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage.

Damian Bertoni¹, Maxim Tsenkov¹, Paulyna Magana¹

¹European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, CB10 1SD,United Kingdom.

Nucleic Acids Research

|November 22, 2025

Summary

This summary is machine-generated.

The AlphaFold Protein Structure Database (AFDB) now includes updated protein structures and a redesigned interface for easier exploration. This enhanced resource supports structural biology research by providing access to millions of protein predictions.

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Area of Science:

Structural biology
Bioinformatics
Computational biology

Background:

The AlphaFold Protein Structure Database (AFDB) is a key resource for accessing protein structure predictions.
It has been widely adopted in life sciences research and integrated into various bioinformatics tools.
Previous versions required updates to incorporate new data and improve user experience.

Purpose of the Study:

To update the AlphaFold Protein Structure Database (AFDB) with the latest UniProt release (2025_03).
To redesign the AFDB entry page for improved usability, accessibility, and structural interpretation.
To expand structural coverage and enhance data accessibility.

Main Methods:

Database update aligning with UniProt 2025_03 release.
Redesign of the entry page with integrated annotations and an interactive 3D viewer.
Inclusion of isoforms and multiple sequence alignments in structural coverage.

Main Results:

The AFDB is updated to UniProt 2025_03, providing access to millions of high-accuracy protein structure predictions.
A redesigned entry page features integrated annotations, an interactive 3D viewer, and dedicated tabs for domains and summaries.
Expanded structural coverage now includes isoforms and multiple sequence alignments.

Conclusions:

The updated AFDB enhances usability and accessibility for researchers.
The database remains a vital, sustainable resource for exploring protein sequence-structure relationships.
New features facilitate deeper structural interpretation and data integration.