StrBioLib：一个用于开发定制计算结构生物学应用程序的Java库。
StrBioLib: a Java library for development of custom computational structural biology applications.
作者信息
Chandonia John-Marc
机构信息
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
出版信息
Bioinformatics. 2007 Aug 1;23(15):2018-20. doi: 10.1093/bioinformatics/btm269. Epub 2007 May 30.
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/
摘要
StrBioLib是一个Java类库，对开发用于计算结构生物学研究的软件很有用。StrBioLib包含用于表示和操作蛋白质结构、生物聚合物序列、生物聚合物序列集以及基于序列或结构的生物聚合物之间比对的类。提供了与常用生物信息学应用程序交互的接口，包括（psi）-blast、Modeller、Muscle和Primer3，还提供了用于读取和写入许多用于表示生物信息数据的文件格式的工具。该库包括一个具有多种训练算法的通用神经网络对象、Hooke和Jeeves非线性优化算法以及用于高效C风格字符串解析和格式化的工具。StrBioLib是Pred2ary二级结构预测程序的基础，用于构建用于序列和结构分析的星历表，并且已在许多较小的项目中得到广泛测试。示例和文档可在以下网站获取。
可用性
StrBioLib可根据GNU LGPL许可条款从http://strbio.sourceforge.net/获得
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