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Title: StrBioLib: a Java library for development of custom computationalstructural biology applications

Abstract

Summary: StrBioLib is a library of Java classes useful fordeveloping software for computational structural biology research.StrBioLib contains classes to represent and manipulate proteinstructures, biopolymer sequences, sets of biopolymer sequences, andalignments between biopolymers based on either sequence or structure.Interfaces are provided to interact with commonly used bioinformaticsapplications, including (PSI)-BLAST, MODELLER, MUSCLE, and Primer3, andtools are provided to read and write many file formats used to representbioinformatic data. The library includes a general-purpose neural networkobject with multiple training algorithms, the Hooke and Jeeves nonlinearoptimization algorithm, and tools for efficient C-style string parsingand formatting. StrBioLib is the basis for the Pred2ary secondarystructure prediction program, is used to build the ASTRAL compendium forsequence and structure analysis, and has been extensively tested throughuse in many smaller projects. Examples and documentation are available atthe site below.Availability: StrBioLib may be obtained under the terms ofthe GNU LGPL license from http://strbio.sourceforge.net/Contact:JMChandonia@lbl.gov

Authors:
Publication Date:
Research Org.:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org.:
USDOE Director, Office of Science; National Institutes ofHealth
OSTI Identifier:
922728
Report Number(s):
LBNL-62661
R&D Project: GTL3JC; BnR: KP1102010; TRN: US200803%%532
DOE Contract Number:  
DE-AC02-05CH11231; NIHR01-GM39900, R01-GM073109, AND1-P50-GM62412
Resource Type:
Journal Article
Resource Relation:
Journal Name: Bioinformatics; Journal Volume: 23; Journal Issue: 15; Related Information: Journal Publication Date: 2007
Country of Publication:
United States
Language:
English
Subject:
99; 59; 60; ALGORITHMS; AVAILABILITY; BIOLOGY; DOCUMENTATION; FORECASTING; JAVA; NEURAL NETWORKS; OPTIMIZATION; PROTEIN STRUCTURE; TRAINING; java library structural biology optimization lgpl neuralnetwork

Citation Formats

Chandonia, John-Marc. StrBioLib: a Java library for development of custom computationalstructural biology applications. United States: N. p., 2007. Web. doi:10.1093/bioinformatics/btm269.
Chandonia, John-Marc. StrBioLib: a Java library for development of custom computationalstructural biology applications. United States. doi:10.1093/bioinformatics/btm269.
Chandonia, John-Marc. Mon . "StrBioLib: a Java library for development of custom computationalstructural biology applications". United States. doi:10.1093/bioinformatics/btm269.
@article{osti_922728,
title = {StrBioLib: a Java library for development of custom computationalstructural biology applications},
author = {Chandonia, John-Marc},
abstractNote = {Summary: StrBioLib is a library of Java classes useful fordeveloping software for computational structural biology research.StrBioLib contains classes to represent and manipulate proteinstructures, biopolymer sequences, sets of biopolymer sequences, andalignments between biopolymers based on either sequence or structure.Interfaces are provided to interact with commonly used bioinformaticsapplications, including (PSI)-BLAST, MODELLER, MUSCLE, and Primer3, andtools are provided to read and write many file formats used to representbioinformatic data. The library includes a general-purpose neural networkobject with multiple training algorithms, the Hooke and Jeeves nonlinearoptimization algorithm, and tools for efficient C-style string parsingand formatting. StrBioLib is the basis for the Pred2ary secondarystructure prediction program, is used to build the ASTRAL compendium forsequence and structure analysis, and has been extensively tested throughuse in many smaller projects. Examples and documentation are available atthe site below.Availability: StrBioLib may be obtained under the terms ofthe GNU LGPL license from http://strbio.sourceforge.net/Contact:JMChandonia@lbl.gov},
doi = {10.1093/bioinformatics/btm269},
journal = {Bioinformatics},
number = 15,
volume = 23,
place = {United States},
year = {Mon May 14 00:00:00 EDT 2007},
month = {Mon May 14 00:00:00 EDT 2007}
}