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Protein and Protein Structure02:15

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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.
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Determining Membrane Protein Topology Using Fluorescence Protease Protection FPP
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ProLego: tool for extracting and visualizing topological modules in protein structures.

Taushif Khan1, Shailesh Kumar Panday2, Indira Ghosh2

  • 1School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India. taushifkhan@gmail.com.

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|May 6, 2018
PubMed
Summary
This summary is machine-generated.

ProLego is a new server application that helps protein designers explore protein topology space efficiently. It aids in reducing the search space by analyzing protein structures and comparing them against an extensive database.

Keywords:
Protein Graph.Protein topologyServer application.Topology comparisons.Visualization.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Protein Engineering

Background:

  • Protein design relies heavily on accurate backbone topology selection for efficient structure searching.
  • Understanding and utilizing protein topology is crucial for reducing the structural search space in protein design.

Purpose of the Study:

  • To introduce ProLego, a server application designed for exploring protein topology.
  • To provide an intuitive and efficient method for scanning the protein topology space.

Main Methods:

  • Development of an in-house "topological representation" for extracting protein topology from structures.
  • Implementation of an automated pipeline for topology extraction and comparison.
  • Creation of an extensive, non-redundant protein topology database (ProLegoDB).

Main Results:

  • ProLego enables the extraction of topological representations (topology strings) from protein structures.
  • The server compares extracted topologies against ProLegoDB and identifies constituent topological modules.
  • Interactive topology visualization graphs are provided within the platform.

Conclusions:

  • ProLego offers a comprehensive approach to scanning and visualizing protein topology.
  • The server facilitates exploration of protein topology space with an extensive database.
  • ProLego is accessible at http://www.proteinlego.com for protein design applications.