结构基因组学：用于结构分析的计算方法。
Structural genomics: computational methods for structure analysis.
作者信息
Goldsmith-Fischman Sharon, Honig Barry
机构信息
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.
出版信息
Protein Sci. 2003 Sep;12(9):1813-21. doi: 10.1110/ps.0242903.
Abstract
The success of structural genomics initiatives requires the development and application of tools for structure analysis, prediction, and annotation. In this paper we review recent developments in these areas; specifically structure alignment, the detection of remote homologs and analogs, homology modeling and the use of structures to predict function. We also discuss various rationales for structural genomics initiatives. These include the structure-based clustering of sequence space and genome-wide function assignment. It is also argued that structural genomics can be integrated into more traditional biological research if specific biological questions are included in target selection strategies.
摘要
结构基因组学计划的成功需要开发和应用用于结构分析、预测及注释的工具。在本文中，我们综述了这些领域的最新进展；具体包括结构比对、远源同源物和类似物的检测、同源建模以及利用结构预测功能。我们还讨论了结构基因组学计划的各种基本原理。这些原理包括基于结构的序列空间聚类和全基因组功能分配。我们还认为，如果在目标选择策略中纳入特定的生物学问题，结构基因组学可以融入更传统的生物学研究中。
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本文引用的文献
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2
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Protein Sci. 2002 Nov;11(11):2606-21. doi: 10.1110/ps.0215902.
3
A new method to detect related function among proteins independent of sequence and fold homology.一种独立于序列和折叠同源性来检测蛋白质间相关功能的新方法。
J Mol Biol. 2002 Oct 18;323(2):387-406. doi: 10.1016/s0022-2836(02)00811-2.
4
ProDom: automated clustering of homologous domains.ProDom：同源结构域的自动聚类
Brief Bioinform. 2002 Sep;3(3):246-51. doi: 10.1093/bib/3.3.246.
5
The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs.使用结构信息来提高比对准确性并不能帮助使用轮廓隐马尔可夫模型进行同源物检测。
Bioinformatics. 2002 Sep;18(9):1243-9. doi: 10.1093/bioinformatics/18.9.1243.
6
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