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Protein and Protein Structure02:15

Protein and Protein Structure

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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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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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PDBparam: Online Resource for Computing Structural Parameters of Proteins.

R Nagarajan1, A Archana1, A Mary Thangakani2

  • 1Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.

Bioinformatics and Biology Insights
|June 23, 2016
PubMed
Summary
This summary is machine-generated.

A new web tool, PDBparam, calculates over 50 structure-based features for proteins. This tool aids in understanding protein structure-function relationships and analyzing protein structures effectively.

Keywords:
binding sitesphysicochemical propertiesprotein three-dimensional structuresecondary structure propensity

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Area of Science:

  • Molecular Biology
  • Computational Biology
  • Biophysics

Background:

  • Understanding the protein structure-function relationship is crucial in molecular and computational biology.
  • Structure-based parameters are key to linking protein structure with its function.
  • Existing tools lack a comprehensive set of structure-based features for protein analysis.

Purpose of the Study:

  • To develop a web-based tool, PDBparam, for calculating a wide range of structure-based features from protein 3D structures.
  • To provide a centralized resource for over 50 distinct protein structural and physicochemical features.
  • To facilitate the analysis of protein structures and enhance the understanding of structure-function relationships.

Main Methods:

  • Development of a web server (PDBparam) accessible at http://www.iitm.ac.in/bioinfo/pdbparam/.
  • Implementation of algorithms to compute >50 structure-based features from protein 3D structures.
  • Classification of features into four categories: interresidue interactions, secondary structure propensities, physicochemical properties, and binding site identification.

Main Results:

  • PDBparam computes over 50 structure-based features, including interresidue interactions (contact order, long-range order), secondary structure propensities (alpha-helix, beta-sheet), physicochemical properties (hydrophobicity, buriedness), and binding site residues.
  • The tool categorizes features into interresidue interactions, secondary structure propensities, physicochemical properties, and binding site identification.
  • The PDBparam server is freely available for public use.

Conclusions:

  • PDBparam is an effective, comprehensive web-based tool for analyzing protein structures.
  • The tool provides valuable insights into protein structure-function relationships by calculating numerous structure-based features.
  • PDBparam serves as a significant resource for researchers in molecular biology, computational biology, and related fields.