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

Title:
StrBioLib: a Java library for development of custom computational structural biology applications.
Authors:
Chandonia JM; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. JMChandonia@lbl.gov
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2007 Aug 01; Vol. 23 (15), pp. 2018-20. Date of Electronic Publication: 2007 May 30.
Publication Type:
Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Models, Biological* , Programming Languages* , Software* , User-Computer Interface*, Biopolymers/*chemistry , Biopolymers/*genetics , Systems Biology/*methods, Biopolymers/metabolism ; Computer Simulation
References:
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Grant Information:
P50 GM062412 United States GM NIGMS NIH HHS; R01 GM073109 United States GM NIGMS NIH HHS; 1-P50-GM62412 United States GM NIGMS NIH HHS; R01-GM073109 United States GM NIGMS NIH HHS; R01-GM39900 United States GM NIGMS NIH HHS
Substance Nomenclature:
0 (Biopolymers)
Entry Date(s):
Date Created: 20070601 Date Completed: 20070911 Latest Revision: 20181113
Update Code:
20250114
PubMed Central ID:
PMC4566930
DOI:
10.1093/bioinformatics/btm269
PMID:
17537750
Database:
MEDLINE

Weitere Informationen

Summary: 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.
Availability: StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/