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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 Organization01:13

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 and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Protein Folding01:22

Protein Folding

Overview

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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 structure prediction by pro-Sp3-TASSER.

Hongyi Zhou1, Jeffrey Skolnick

  • 1Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA.

Biophysical Journal
|March 18, 2009
PubMed
Summary

The pro-sp3-TASSER algorithm improves automated protein structure prediction accuracy over MetaTASSER. This new method enhances the identification of foldable protein models, especially for challenging targets.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Accurate protein structure prediction is crucial for understanding biological function.
  • Existing automated methods like MetaTASSER have limitations, particularly for difficult targets.

Purpose of the Study:

  • To introduce and evaluate pro-sp3-TASSER, an enhanced automated protein structure prediction algorithm.
  • To benchmark pro-sp3-TASSER against MetaTASSER using a diverse set of protein targets.

Main Methods:

  • Utilized five scoring functions from PROSPECTOR_3 and SP(3) for template identification.
  • Integrated contact and distance restraints from top templates for refinement via TASSER simulations.
  • Employed TASSER-QA for model selection and iterative refinement, including parametric alignment for challenging targets.

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Main Results:

  • pro-sp3-TASSER demonstrated statistically significant improvements in TM-score across easy (2.1%), medium (2.8%), and hard (2.2%) targets compared to MetaTASSER.
  • The number of correctly predicted foldable protein structures increased, with notable relative gains of 10% for medium and 15% for hard targets.
  • The algorithm successfully generated an ensemble of models, with final selection based on TASSER-QA evaluation.

Conclusions:

  • pro-sp3-TASSER represents a significant advancement in automated protein structure prediction.
  • The method shows improved performance, particularly for protein targets with less reliable template information.
  • An accessible web server and source code are available for broader use and research.