title: StrBioLib: a Java library for development of custom computational structural biology applications.
abstract: CONCLUSIONS
  StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves non-linear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the astral compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below.
  
  
  BACKGROUND
  StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. JMChandonia@lbl.gov
authors.forename: John-Marc
authors.initials: JM
authors.lastname: Chandonia
mesh_terms: D001704:Biopolymers / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D003198:Computer Simulation; D008954:Models, Biological; D011381:Programming Languages; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014584:User-Computer Interface
chemical_list: D001704:Biopolymers