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Protein Families02:47

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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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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.
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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
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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.
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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein

Niharika Saraf1, Vishvesh Karthik1, Gaurav Sharma2

  • 1Microbial Genomics and Evolution Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Sangareddy, Telangana, India.

BMC Bioinformatics
|November 26, 2025
PubMed
Summary

The AlphaFoldDB Structure Extractor tool simplifies downloading predicted protein structures from the AlphaFold Database. It supports various identifiers and formats, enabling efficient bulk downloads for researchers.

Keywords:
API toolkitAlphaFoldDBBioinformaticsComputational biologyNCBIOpen accessProtein structureStructural genomicsUniProt

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Genomics

Background:

  • The AlphaFold Database contains numerous predicted protein structures, but accessing them in bulk can be challenging.
  • Existing methods often have limitations regarding the number of structures or model organisms that can be accessed.

Purpose of the Study:

  • To develop an open-access web server and API toolkit for efficient bulk downloading of protein structures from the AlphaFold Database.
  • To overcome limitations in accessing structures beyond a restricted set of model organisms and a threshold number.

Main Methods:

  • The AlphaFoldDB Structure Extractor accepts diverse input identifiers like NCBI Taxonomy ID, RefSeq, locus tags, and UniProt/AlphaFold accessions.
  • It provides structure files in PDB, mmCIF, bCIF, or PAE JSON formats and includes an ID mapping utility.
  • An API methodology is available for programmatic access and integration into bioinformatics pipelines.

Main Results:

  • The tool successfully facilitates bulk downloads of predicted protein structures from the AlphaFold Database.
  • It supports various input identifiers and output formats, including PDB, mmCIF, bCIF, and PAE JSON.
  • An ID mapping file is generated to trace input identifiers, and unmapped IDs are reported separately.

Conclusions:

  • The AlphaFoldDB Structure Extractor streamlines protein structure procurement from the AlphaFold Database.
  • It empowers researchers in structural and functional genomics by simplifying data access with minimal computational expertise.