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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
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 Organization01:13

Protein Organization

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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-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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Updated: Jul 4, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Protein contact order prediction from primary sequences.

Yi Shi1, Jianjun Zhou, David Arndt

  • 1Department of Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada. ys3@cs.ualberta.ca

BMC Bioinformatics
|June 3, 2008
PubMed
Summary
This summary is machine-generated.

Predicting protein contact order from amino acid sequences is now possible. New methods correlate sequence features with contact order, enabling predictions without 3D structures.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein science

Background:

  • Contact order is a key topological descriptor influencing protein folding rates and transition states.
  • It's used in protein structure prediction but requires known 3D structures for calculation.
  • No effective methods exist for predicting contact order from sequences alone.

Purpose of the Study:

  • To develop effective methods for predicting protein contact order directly from amino acid sequences.
  • To create a robust calculator for contact order from PDB coordinates.
  • To provide a web server for these newly developed tools.

Main Methods:

  • Developed prediction methods based on weighted linear combinations of predicted secondary structure content and amino acid composition.
  • Employed sequence similarity to known 3D structures for prediction.
  • Created a robust PDB coordinate-based contact order calculator.

Main Results:

  • Achieved correlation coefficients of 0.857-0.870 using secondary structure and amino acid composition.
  • Reached a correlation coefficient of 0.977 with the sequence similarity method.
  • The PDB calculator successfully processes over 99% of PDB files.

Conclusions:

  • Protein contact order can be accurately predicted from primary sequences, even without 3D structural information.
  • Key predictive factors include alpha-helix content, beta-strand content, and protein sequence length.
  • The developed tools are available via a web server for broader accessibility.