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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.
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BiopLib and BiopTools--a C programming library and toolset for manipulating protein structure.

Craig T Porter1, Andrew C R Martin1

  • 1Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.

Bioinformatics (Oxford, England)
|September 2, 2015
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Summary
This summary is machine-generated.

BiopLib is a C library and BiopTools are command-line tools for protein structure manipulation. They handle PDB and PDBML formats, offering features like residue renumbering and solvent accessibility calculations.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Protein structure data is crucial for biological research.
  • Efficient tools are needed for manipulating and analyzing protein structures.
  • Handling diverse file formats like PDB and PDBML can be challenging.

Purpose of the Study:

  • To introduce BiopLib, a C programming library for protein structure manipulation.
  • To present BiopTools, a suite of command-line tools utilizing BiopLib.
  • To provide flexible and robust tools for handling protein structural data.

Main Methods:

  • BiopLib is implemented in ANSI C, featuring a robust PDB parser.
  • The library supports PDBML (XML) and standard PDB file formats, including compressed files.
  • BiopTools offers command-line utilities for tasks such as renumbering and solvent accessibility calculation.

Main Results:

  • BiopLib provides a flexible data structure for protein information (atoms, residues, chains).
  • BiopTools functions as a filter, processing PDB/PDBML files for various analyses.
  • The tools transparently handle PDBML and compressed PDB files.

Conclusions:

  • BiopLib and BiopTools offer a mature, open-source solution for protein structure analysis.
  • The library and tools are designed for flexibility and ease of use in bioinformatics workflows.
  • Availability under GNU Public License and on GitHub facilitates widespread adoption.