三维注释。PINTS：非同源三级结构中的模式。
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.
作者信息
Stark Alexander, Russell Robert B
机构信息
EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
出版信息
Nucleic Acids Res. 2003 Jul 1;31(13):3341-4. doi: 10.1093/nar/gkg506.
Abstract
The detection of local structural patterns in proteins (e.g. active sites) can provide insights into protein function in the absence of sequence or fold similarity. Methods to detect such similarities are key during structural annotation, for example with results from Structural Genomics initiatives. PINTS (Patterns in Non-homologous Tertiary Structures, http://pints.embl.de) performs database searches for such patterns and most importantly provides a measure of statistical significance for any similarity uncovered. To aid functional annotation of proteins, we allow comparisons of pre-defined patterns against databases of complete structures and of entire structures to databases of particular residues likely to be functionally important.
摘要
在缺乏序列或折叠相似性的情况下，检测蛋白质中的局部结构模式（如活性位点）有助于深入了解蛋白质功能。检测此类相似性的方法在结构注释过程中至关重要，例如对于结构基因组学计划的结果而言。PINTS（非同源三级结构中的模式，http://pints.embl.de）可针对此类模式进行数据库搜索，最重要的是，对于所发现的任何相似性，它都能提供统计显著性的度量。为了辅助蛋白质的功能注释，我们允许将预定义模式与完整结构数据库进行比较，并将整个结构与可能具有重要功能的特定残基数据库进行比较。
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本文引用的文献
1
Raster3D Version 2.0. A program for photorealistic molecular graphics.光栅3D版本2.0。一个用于逼真分子图形的程序。
Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):869-73. doi: 10.1107/S0907444994006396.
2
A model for statistical significance of local similarities in structure.一种用于结构局部相似性统计显著性的模型。
J Mol Biol. 2003 Mar 7;326(5):1307-16. doi: 10.1016/s0022-2836(03)00045-7.
3
Getting the most from PSI-BLAST.充分利用PSI-BLAST。
Trends Biochem Sci. 2002 Mar;27(3):161-4. doi: 10.1016/s0968-0004(01)02039-4.
4
An NMR approach to structural proteomics.一种用于结构蛋白质组学的核磁共振方法。
Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):1825-30. doi: 10.1073/pnas.042684599.
5
Crystal structures of a novel ferric reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus and its complex with NADP+.来自嗜热古菌嗜热栖热放线菌的一种新型铁还原酶及其与NADP⁺复合物的晶体结构。
Structure. 2001 Apr 4;9(4):311-9. doi: 10.1016/s0969-2126(01)00589-5.
6
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements.利用基于组成的统计方法和其他改进措施提高PSI-BLAST蛋白质数据库搜索的准确性。
Nucleic Acids Res. 2001 Jul 15;29(14):2994-3005. doi: 10.1093/nar/29.14.2994.
7
Determination of protein function, evolution and interactions by structural genomics.通过结构基因组学确定蛋白质的功能、进化及相互作用。
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8
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From structure to function: approaches and limitations.从结构到功能：方法与局限
Nat Struct Biol. 2000 Nov;7 Suppl:991-4. doi: 10.1038/80784.
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