一种检测蛋白质中结构域的方法。
A procedure for detecting structural domains in proteins.
作者信息
Swindells M B
机构信息
Protein Engineering Research Institute, Osaka, Japan.
出版信息
Protein Sci. 1995 Jan;4(1):103-12. doi: 10.1002/pro.5560040113.
Abstract
A procedure is described for detecting domains in proteins of known structure. The method is based on the intuitively simple idea that each domain should contain an identifiable hydrophobic core. By applying the algorithm described in the companion paper (Swindells MB, 1995, Protein Sci 4:93-102) to identify distinct cores in multi-domain proteins, one can use this information to determine both the number and the location of the constituent domains. Tests have shown the procedure to be effective on a number of examples, even when the domains are discontinuous along the sequence. However, deficiencies also occur when hydrophobic cores from different domains continue through the interface region and join one another.
摘要
本文描述了一种用于检测已知结构蛋白质中结构域的方法。该方法基于一个直观简单的理念，即每个结构域都应包含一个可识别的疏水核心。通过应用配套论文（Swindells MB，1995，Protein Sci 4：93 - 102）中描述的算法来识别多结构域蛋白质中的不同核心，人们可以利用这些信息来确定组成结构域的数量和位置。测试表明，该方法在多个实例中均有效，即使结构域在序列上是不连续的。然而，当来自不同结构域的疏水核心穿过界面区域并相互连接时，也会出现不足之处。
相似文献
1
A procedure for detecting structural domains in proteins.一种检测蛋白质中结构域的方法。
Protein Sci. 1995 Jan;4(1):103-12. doi: 10.1002/pro.5560040113.
2
Inferring boundary information of discontinuous-domain proteins.推断不连续结构域蛋白质的边界信息。
IEEE Trans Nanobioscience. 2008 Sep;7(3):200-5. doi: 10.1109/TNB.2008.2002283.
3
A procedure for the automatic determination of hydrophobic cores in protein structures.一种自动确定蛋白质结构中疏水核心的方法。
Protein Sci. 1995 Jan;4(1):93-102. doi: 10.1002/pro.5560040112.
4
SnapDRAGON: a method to delineate protein structural domains from sequence data.SnapDRAGON：一种从序列数据中描绘蛋白质结构域的方法。
J Mol Biol. 2002 Feb 22;316(3):839-51. doi: 10.1006/jmbi.2001.5387.
5
A comprehensive and non-redundant database of protein domain movements.一个全面且无冗余的蛋白质结构域运动数据库。
Bioinformatics. 2005 Jun 15;21(12):2832-8. doi: 10.1093/bioinformatics/bti420. Epub 2005 Mar 31.
6
Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions.连续和不连续结构域：一种自动生成可靠蛋白质结构域定义的算法
Protein Sci. 1995 May;4(5):872-84. doi: 10.1002/pro.5560040507.
7
Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin.利用液态核磁共振测量的偶极耦合来确定蛋白质中的取向域：负载β-环糊精的麦芽糖糊精结合蛋白在溶液和晶体形式中的差异。
J Mol Biol. 2000 Feb 4;295(5):1265-73. doi: 10.1006/jmbi.1999.3430.
8
Armadillo: domain boundary prediction by amino acid composition.犰狳：基于氨基酸组成的结构域边界预测
J Mol Biol. 2005 Jul 29;350(5):1061-73. doi: 10.1016/j.jmb.2005.05.037.
9
Identification of linker regions and domain borders of the transcription activator protein NtrC from Escherichia coli by limited proteolysis, in-gel digestion, and mass spectrometry.通过有限蛋白酶解、凝胶内消化和质谱法鉴定大肠杆菌转录激活蛋白NtrC的连接区和结构域边界。
Biochemistry. 1999 Aug 24;38(34):11012-20. doi: 10.1021/bi990781k.
10
An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins.一种涉及对二级结构进行聚类分析以识别蛋白质结构域的自动化方法。
Protein Sci. 1995 Mar;4(3):506-20. doi: 10.1002/pro.5560040317.
引用本文的文献
1
Merizo: a rapid and accurate protein domain segmentation method using invariant point attention.Merizo：一种使用不变点注意力的快速准确的蛋白质结构域分割方法。
Nat Commun. 2023 Dec 19;14(1):8445. doi: 10.1038/s41467-023-43934-4.
2
Assignment of structural domains in proteins using diffusion kernels on graphs.使用图上的扩散核来分配蛋白质中的结构域。
BMC Bioinformatics. 2022 Sep 8;23(1):369. doi: 10.1186/s12859-022-04902-9.
3
Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction.基于共进化的结构预测拓展同源检测的视野。
J Mol Biol. 2021 Oct 1;433(20):167106. doi: 10.1016/j.jmb.2021.167106. Epub 2021 Jun 15.
4
Co-evolution techniques are reshaping the way we do structural bioinformatics.协同进化技术正在重塑我们进行结构生物信息学研究的方式。
F1000Res. 2017 Jul 25;6:1224. doi: 10.12688/f1000research.11543.1. eCollection 2017.
5
The history of the CATH structural classification of protein domains.蛋白质结构域的CATH结构分类历史。
Biochimie. 2015 Dec;119:209-17. doi: 10.1016/j.biochi.2015.08.004. Epub 2015 Aug 4.
6
IS-Dom: a dataset of independent structural domains automatically delineated from protein structures.IS-Dom：一个从蛋白质结构中自动划分的独立结构域数据集。
J Comput Aided Mol Des. 2013 May;27(5):419-26. doi: 10.1007/s10822-013-9654-6. Epub 2013 May 29.
7
Protein domain assignment from the recurrence of locally similar structures.基于局部相似结构的重复对蛋白质结构域进行分配。
Proteins. 2011 Mar;79(3):853-66. doi: 10.1002/prot.22923. Epub 2010 Dec 22.
8
Could protein tertiary structure influence mammary transgene expression more than tissue specific codon usage?蛋白质三级结构是否比组织特异性密码子使用更能影响乳腺转基因表达？
Transgenic Res. 2010 Aug;19(4):519-33. doi: 10.1007/s11248-010-9411-8. Epub 2010 Jun 19.
9
A database of domain definitions for proteins with complex interdomain geometry.具有复杂结构域间几何形状的蛋白质结构域定义数据库。
PLoS One. 2009;4(4):e5084. doi: 10.1371/journal.pone.0005084. Epub 2009 Apr 8.
10
Analyses of domains and domain fusions in human proto-oncogenes.人类原癌基因中结构域及结构域融合的分析。
BMC Bioinformatics. 2009 Mar 17;10:88. doi: 10.1186/1471-2105-10-88.
本文引用的文献
1
Identification and classification of protein fold families.蛋白质折叠家族的识别与分类。
Protein Eng. 1993 Jul;6(5):485-500. doi: 10.1093/protein/6.5.485.
2
Protein structure comparison by alignment of distance matrices.通过距离矩阵比对进行蛋白质结构比较。
J Mol Biol. 1993 Sep 5;233(1):123-38. doi: 10.1006/jmbi.1993.1489.
3
Binary discontinuous compact protein domains.二元不连续紧密蛋白结构域
Protein Eng. 1994 Mar;7(3):335-40. doi: 10.1093/protein/7.3.335.
4
Parser for protein folding units.蛋白质折叠单元解析器。
Proteins. 1994 Jul;19(3):256-68. doi: 10.1002/prot.340190309.
5
A procedure for the automatic determination of hydrophobic cores in protein structures.一种自动确定蛋白质结构中疏水核心的方法。
Protein Sci. 1995 Jan;4(1):93-102. doi: 10.1002/pro.5560040112.
6
Location of structural domains in protein.蛋白质中结构域的位置。
Biochemistry. 1981 Nov 10;20(23):6544-52. doi: 10.1021/bi00526a005.
7
Structure of thermolysin refined at 1.6 A resolution.在1.6埃分辨率下精修的嗜热菌蛋白酶结构。
J Mol Biol. 1982 Oct 5;160(4):623-39. doi: 10.1016/0022-2836(82)90319-9.
8
The anatomy and taxonomy of protein structure.蛋白质结构的解剖学与分类学。
Adv Protein Chem. 1981;34:167-339. doi: 10.1016/s0065-3233(08)60520-3.
9
Structure of papain refined at 1.65 A resolution.木瓜蛋白酶结构在1.65埃分辨率下的精修。
J Mol Biol. 1984 Oct 25;179(2):233-56. doi: 10.1016/0022-2836(84)90467-4.
10
The prediction of protein domains.蛋白质结构域的预测。
Biochim Biophys Acta. 1984 Oct 23;790(2):117-24. doi: 10.1016/0167-4838(84)90214-0.
Zotero 插件