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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
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

pKNOT v.2: the protein KNOT web server.

Yan-Long Lai1, Chih-Chieh Chen, Jenn-Kang Hwang

  • 1Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 30068, Taiwan, Republic of China.

Nucleic Acids Research
|June 14, 2012
PubMed
Summary
This summary is machine-generated.

The pKNOT v.2 web server now analyzes knotted proteins directly from sequences using homology modeling. This updated tool enhances research into protein knot topology and folding mechanisms.

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Last Updated: May 21, 2026

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Knotted proteins exhibit unique topological properties and complex folding pathways, attracting significant research interest.
  • Existing tools like the pKNOT server primarily analyze 3D protein structures, lacking direct sequence-based analysis.

Purpose of the Study:

  • To enhance the pKNOT web server (v.2) to accept protein sequences for knot analysis.
  • To provide a convenient platform for biologists to study knotted proteins from sequence data.

Main Methods:

  • Implemented a homology modeling tool to enable sequence-based analysis.
  • Updated the knotted protein database using current Protein Data Bank (PDB) data through automated and manual curation.

Main Results:

  • The pKNOT v.2 server now accepts protein sequences, 3D structures, or PDB IDs.
  • An updated database of knotted proteins is integrated into the server.

Conclusions:

  • The enhanced pKNOT v.2 server offers extended functionalities for researching knotted proteins.
  • This tool will benefit biologists studying protein knot topology and folding mechanisms.