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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
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-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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Related Experiment Video

Updated: May 30, 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

Improving protein structure prediction using multiple sequence-based contact predictions.

Sitao Wu1, Andras Szilagyi, Yang Zhang

  • 1Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS 66047, USA.

Structure (London, England : 1993)
|August 11, 2011
PubMed
Summary
This summary is machine-generated.

We developed accurate protein contact predictors to improve protein structure prediction. This method significantly enhances model quality, especially for challenging free-modeling targets.

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein structure prediction is crucial for understanding biological function.
  • Accurate residue-residue contact predictions are essential for determining protein topology.
  • Current sequence-based ab initio contact predictions lack sufficient accuracy for reliable structure prediction.

Purpose of the Study:

  • To improve the accuracy of protein structure prediction, particularly for targets lacking homologous templates.
  • To integrate enhanced contact prediction methods into the I-TASSER simulation pipeline.
  • To assess the impact of improved contact predictions on the quality of predicted protein models.

Main Methods:

  • Developed a composite set of nine Support Vector Machine (SVM)-based contact predictors.
  • Integrated these predictors with sparse template contact restraints in I-TASSER simulations.
  • Tested the strategy on 273 nonhomologous protein targets.

Main Results:

  • Observed significant improvements in I-TASSER model quality for both easy and hard targets (p < 0.00001 and p < 0.001, respectively).
  • Achieved template modeling score increases exceeding 30% in several cases, enabling the prediction of previously "nonfoldable" targets.
  • In CASP9, I-TASSER models for free-modeling (FM) targets showed superior GDT-scores compared to other top servers.

Conclusions:

  • The developed composite contact prediction strategy offers a novel approach to enhance protein structure prediction accuracy.
  • This method is particularly effective for free-modeling targets, overcoming limitations of traditional template-based modeling.
  • The findings pave the way for more reliable ab initio protein structure modeling.