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StrBioLib: a Java library for development of custom computational structural biology applications.

John-Marc Chandonia1

  • 1Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. JMChandonia@lbl.gov

Bioinformatics (Oxford, England)
|June 1, 2007
PubMed
Summary
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StrBioLib is a Java library for computational structural biology, offering tools for protein structures, sequences, and alignments. It integrates with bioinformatics applications and supports data manipulation for research.

Area of Science:

  • Computational structural biology
  • Bioinformatics software development

Background:

  • StrBioLib is a Java library available under the GNU LGPL license.
  • It is accessible from http://strbio.sourceforge.net/.

Purpose of the Study:

  • To provide a comprehensive Java library for computational structural biology research.
  • To facilitate the development of software for analyzing protein structures and biopolymer sequences.

Main Methods:

  • The library includes classes for representing and manipulating protein structures, biopolymer sequences, and alignments.
  • It offers interfaces for common bioinformatics tools like (psi)-blast, modeller, muscle, and Primer3.
  • Includes tools for reading/writing various bioinformatics file formats, a neural network object, optimization algorithms, and string parsing utilities.

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Main Results:

  • StrBioLib supports the representation and manipulation of protein structures, sequences, and alignments.
  • It enables interaction with popular bioinformatics applications and handles diverse data formats.
  • The library has been utilized in developing secondary structure prediction programs and sequence/structure analysis compendiums.

Conclusions:

  • StrBioLib is a versatile Java library for computational structural biology research.
  • It simplifies the development of bioinformatics tools by providing robust data structures and application interfaces.
  • The library's extensive testing and application in various projects demonstrate its utility and reliability.