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Protein Organization01:24

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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.
The primary structure of a protein is its amino acid sequence....
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Toolbox for Protein Structure Prediction.

Daniel Barry Roche1,2,3,4,5, Liam James McGuffin6

  • 1Institut de Biologie Computationnelle, LIRMM, CNRS, Université de Montpellier, Montpellier, France. daniel.roche@lirmm.fr.

Methods in Molecular Biology (Clifton, N.J.)
|November 1, 2015
PubMed
Summary

Predicting protein tertiary structure from amino acid sequences is crucial. This study details the IntFOLD2-TS web server, a cutting-edge tool for accurate protein structure prediction and functional elucidation.

Keywords:
Bioinformatics web server sContinuous Automated Model EvaluatiOn (CAMEO)Critical Assessment of Techniques for Protein Structure Prediction (CASP)Fold recognitionModel quality assessment method sProtein Model Portal (PMP)Protein Structure Initiative (PSI)Protein structureProtein tertiary structure predictionTemplate-based mode lingTemplate-free model ing

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • High-throughput sequencing generates vast amounts of protein sequence data, outpacing experimental structure determination.
  • A significant gap exists between known protein sequences and their solved tertiary structures.
  • In silico protein structure prediction is vital for understanding protein function.

Purpose of the Study:

  • To discuss protein tertiary structure prediction and the CASP competition.
  • To introduce and detail the IntFOLD2-TS web server for tertiary structure prediction.
  • To provide practical guidance and examples for using the IntFOLD2-TS server.

Main Methods:

  • Discussion of protein tertiary structure prediction algorithms.
  • Detailed presentation of the IntFOLD2-TS web server.
  • Step-by-step guide and real-world examples for IntFOLD2-TS usage.

Main Results:

  • IntFOLD2-TS is presented as a cutting-edge method for protein tertiary structure prediction.
  • The study demonstrates the utility of the IntFOLD server in improving structure prediction.
  • Examples showcase how IntFOLD aids in protein functional elucidation.

Conclusions:

  • The IntFOLD2-TS web server offers an advanced solution for protein tertiary structure prediction.
  • This tool can bridge the gap between sequence data and structural knowledge.
  • Accurate structure prediction facilitates deeper understanding of protein function.