StrBioLib: a Java library for development of custom computationalstructural biology applications
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
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE Director, Office of Science; National Institutes ofHealth
- DOE Contract Number:
- DE-AC02-05CH11231; NIHR01-GM39900, R01-GM073109, AND1-P50-GM62412
- OSTI ID:
- 922728
- Report Number(s):
- LBNL-62661; R&D Project: GTL3JC; BnR: KP1102010; TRN: US200803%%532
- Journal Information:
- Bioinformatics, Vol. 23, Issue 15; Related Information: Journal Publication Date: 2007
- Country of Publication:
- United States
- Language:
- English
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