用于分析蛋白质-蛋白质相互作用及界面的现有工具和网络服务器的调查。
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces.
作者信息
Tuncbag Nurcan, Kar Gozde, Keskin Ozlem, Gursoy Attila, Nussinov Ruth
机构信息
Computational Sciences and Engineering Program at Koc University, Istanbul, Turkey.
出版信息
Brief Bioinform. 2009 May;10(3):217-32. doi: 10.1093/bib/bbp001. Epub 2009 Feb 24.
Abstract
The unanimous agreement that cellular processes are (largely) governed by interactions between proteins has led to enormous community efforts culminating in overwhelming information relating to these proteins; to the regulation of their interactions, to the way in which they interact and to the function which is determined by these interactions. These data have been organized in databases and servers. However, to make these really useful, it is essential not only to be aware of these, but in particular to have a working knowledge of which tools to use for a given problem; what are the tool advantages and drawbacks; and no less important how to combine these for a particular goal since usually it is not one tool, but some combination of tool-modules that is needed. This is the goal of this review.
摘要
细胞过程（在很大程度上）由蛋白质之间的相互作用所支配，这一共识促使整个科学界付出了巨大努力，最终产生了与这些蛋白质相关的海量信息，包括它们相互作用的调控、相互作用的方式以及由这些相互作用所决定的功能。这些数据已被整理到数据库和服务器中。然而，要使这些数据真正发挥作用，不仅要了解它们，更重要的是要切实掌握针对特定问题应使用哪些工具；这些工具的优缺点是什么；同样重要的是，如何为实现特定目标而将这些工具结合起来，因为通常需要的不是一种工具，而是工具模块的某种组合。这就是本综述的目标。
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本文引用的文献
1
3did Update: domain-domain and peptide-mediated interactions of known 3D structure.
Nucleic Acids Res. 2009 Jan;37(Database issue):D300-4. doi: 10.1093/nar/gkn690. Epub 2008 Oct 25.
2
Architectures and functional coverage of protein-protein interfaces.
J Mol Biol. 2008 Sep 5;381(3):785-802. doi: 10.1016/j.jmb.2008.04.071. Epub 2008 May 6.
3
Using protein binding site prediction to improve protein docking.
Gene. 2008 Oct 1;422(1-2):14-21. doi: 10.1016/j.gene.2008.06.014. Epub 2008 Jun 14.
4
KFC Server: interactive forecasting of protein interaction hot spots.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W265-9. doi: 10.1093/nar/gkn346. Epub 2008 Jun 6.
5
Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces.
BMC Bioinformatics. 2008 May 12;9:234. doi: 10.1186/1471-2105-9-234.
6
An in vivo map of the yeast protein interactome.
Science. 2008 Jun 13;320(5882):1465-70. doi: 10.1126/science.1153878. Epub 2008 May 8.
7
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W260-4. doi: 10.1093/nar/gkn185. Epub 2008 May 8.
8
The RosettaDock server for local protein-protein docking.
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W233-8. doi: 10.1093/nar/gkn216. Epub 2008 Apr 28.
9
Characterization and prediction of protein interfaces to infer protein-protein interaction networks.
Curr Pharm Biotechnol. 2008 Apr;9(2):67-76. doi: 10.2174/138920108783955191.
10
Alignment of non-covalent interactions at protein-protein interfaces.
PLoS One. 2008 Apr 2;3(4):e1926. doi: 10.1371/journal.pone.0001926.
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