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小木虫论坛-学术科研互动平台 » 生物医药区 » 分子生物 » 生物信息 » 如何查找某一蛋白质结构域的结合蛋白或者基因？
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moshangchenx

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[求助] 如何查找某一蛋白质结构域的结合蛋白或者基因？ 已有2人参与

如何查找某一蛋白质结构域的结合蛋白或者基因？
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科研无止境，我心成蹉跎
1楼 2014-08-08 13:31:28
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凌波丽

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DNA和蛋白质序列数据分析工具(第三版）
下载：http://muchong.com/bbs/viewthread.php?tid=7614763

该书对常见的生物信息学软件和数据库都做了通俗的描述和操作指导，很容易上手，楼主可以参考。
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6楼2014-08-13 23:45:32
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bio_sci

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★ ★ ★ ★
感谢参与，应助指数 +1
kx444555: 金币+2, 鼓励交流 2014-08-08 13:50:48
moshangchenx: 金币+2, ★有帮助 2014-08-08 17:46:17
这个得做酵母或者大肠双杂交吧

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2楼2014-08-08 13:35:39
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moshangchenx

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引用回帖:
2楼: Originally posted by bio_sci at 2014-08-08 13:35:39
这个得做酵母或者大肠双杂交吧

您好  有没有生物信息学的方法进行预测呢
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科研无止境，我心成蹉跎
3楼2014-08-08 17:46:48
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凌波丽

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moshangchenx: 金币+8, ★★★★★最佳答案, 非常有用 2014-08-14 20:35:00
西门吹雪170: 金币+5, 鼓励热心回帖交流 2014-08-15 12:55:45
如何查找某一蛋白质结构域的结合蛋白或者基因？

我没有全部理解你的问题，你是不是想问：某一个蛋白质的结构域(domain)或者motif能够与哪些别的蛋白质或者DNA片段相结合？而且要求不是用实验研究方法，要使用生物信息学方法，对吗？
如果我没有猜错的话，你的问题就是要求用生物信息学方法预测或者搜索蛋白质的结构域(domain)或者motif能够与哪些别的蛋白质或者DNA片段相结合及具体位点（序列）。这并不难。

第一个问题：用生物信息学方法预测或者搜索蛋白质的结构域(domain)或者motif能够与哪些别的蛋白质相结合及具体位点（序列）。

I.利用蛋白质-蛋白质相互作用的网上预测软件和数据库:
"2. Database Mining
With the advent of high-throughput testing of protein–protein interactions,it is no longer sufficient to search a bibliographic database like MEDLINE to find out whether two proteins are known to interact. As more and more protein–protein interactions are identified, it is becoming increasingly difficult to access and analyze this information. Several databases are being developed to address this issue. At this time the content overlap between the major databases is not very extensive, and multiple sites should be searched.
A search for your protein of interest will return a list of proteins in the database that interact with the target and some properties of the interaction. In general, you can expect to find fields for alternate names for genes, links to the appropriate entries in sequence databases, some description of protein function, and subcellular localization. A list of methods used to establish the interaction and links to MEDLINE for articles in which the interaction was established are also standard. However, much of this information is incomplete at this time. Most sites include graphical tools that allow you to browse the database by following a chain of interactions and creating a “pathway.”
Searching these resources can produce several benefits. First, you may determine that the interaction you proposed to test has already been reported. In addition, knowledge of a protein’s interactions can guide hypotheses of its function and may suggest interesting ligands.
•A Molecular Interactions Database (MINT; http://cbm.bio.uniroma2.it/mint/index.html) may be a good place to start because it is very easy to navigate, with relatively few options and an easy-to-use graphical interface. It also includesinformation on post-translational modifications and the regions of the proteins involved in an interaction when known.
• The Biomolecular Interaction Network Database (BIND, http://bind.ca/index.phtml) is not quite as easy to navigate as MINT. Like MINT, it lists post-translational modifications and interaction domains for some protein pairs. BIND is notable for its high level of detail for experimental conditions.
• General Repository for Interaction Datasets (GRID, http://biodata.mshri.on.ca/grid/servlet/Index) tends to focus on yeast protein–protein interactions. It can be navigated using an excellent graphical interface, which may also be used as a stand-alone program for generating pathway diagrams. It uses Gene Ontology categories to describe protein function and localization. (The Gene Ontology Consortium [http://www.geneontology.org/] aims to provide a controlled vocabulary for several aspects of the biosciences.)
• One of the notable features of the Database of Interacting Proteins (DIP, http://dip.doe-mbi.ucla.edu/) is the attempt to evaluate the strength of the evidence supporting each interaction. Entries in DIP also have an extensive list of links toother databases, including various protein domain listings. Consider installing the add-on JDIP graphical interface, available at http://dip.doe-mbi.ucla.edu/dip/
jdip.cgi, to make browsing the database easier.

3. Domain Searches and Interaction Predictions
Domains are functional subunits that can confer specific properties on their
host proteins. One such property is the ability to interact with other domains.
522 Masters
For example, SH2 domains can bind phosphotyrosine-containing domains.
There are several well-established databases on the Internet that contain signature motifs for many different domains. Checking your protein against
them can give insight into the possible functions and interaction partners of a
protein.
• InterPro Scan (http://www.ebi.ac.uk/interpro/index.html) allows you to check your protein sequence against multiple motif databases at once, including Pfam and PROSITE, which are two of the largest and most commonly used collections of motifs. Each database differs in the way that motifs are defined and which motifs are included, so scanning multiple databases can improve the sensitivity of your search. The results are hyperlinked to pages that define each domain, summarize what is known about their functional significance, and allow you to search for other proteins with the same domains.
• iSpot (http://cbm.bio.uniroma2.it/ispot/) specifically addresses protein–protein interactions mediated by three common interaction domains. It uses results from published peptide binding studies to predict how well different PDZ, SH3, andWW domain containing proteins will bind to your target sequence.
• Interdom (http://interdom.lit.org.sg/) attempts to predict what protein domains will bind your protein. Given the sequence of your protein, Interdom will identify domains in your protein and report what other domains could interact with them. The program uses a variety of approaches to make these predictions, and will attempt to rank which interactions are most likely. Proteins containing these potential binding domains can be found by following the hyperlink to the Pfam database.
• ScanSite (http://scansite.mit.edu) searches protein sequences for domains and for potential sites of post-translational modification. Please refer to Chapter 30 for a detailed description of this resource."
                                                        From：Haian Fu edits ,Protein-Protein Interactions:Methods and Applications,Humana Press,2004,521-522.
Haian Fu edits ,Protein-Protein Interactions,Humana Press,2004（唯一完整版）下载：
http://muchong.com/bbs/viewthread.php?tid=7764403

II.用分子对接软件，进行蛋白质-蛋白质相互作用预测，请参见：
余俊杰、冯华、梁龙 主编，蛋白质结构预测实验指南，化学工业出版社，2010，可参考其第五章和第六章。

该书下载：http://muchong.com/bbs/viewthread.php?tid=6363934

第二个问题：用生物信息学方法预测或者搜索蛋白质的结构域(domain)或者motif能够与哪些DNA片段相结合及具体位点（序列）。

有很多软件可以执行此操作。具体操作可以看：薛庆中 等 编，DNA和蛋白质序列数据分析工具，科学出版社，2012，第三版，第六章、序列模体的识别和解析。
下载：
1.薛庆中 等 编，DNA和蛋白质序列数据分析工具，科学出版社，2010，第二版，
http://muchong.com/bbs/viewthread.php?tid=6358121
下载后即可阅读。
2.薛庆中 等 编，DNA和蛋白质序列数据分析工具，科学出版社，2012，第三版，
http://muchong.com/bbs/viewthread.php?tid=7614763
下载后好像无法解压，楼主试试看吧，至少“DNA和蛋白质序列数据分析工具(第二版)”肯定能够用，可以在第二版中找一下序列模体的识别和解析的内容。

附录：转录因子数据库与转录因子预测软件

转录因子数据库：
TRANSFAC:
http://www.gene-regulation.com/pub/databses.html
TRRD:
http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/
TFD:
http://www.ifti.org/
JASPAP :
http://jaspar.cgb.ki.se/
DBTSS:
http://dbtess.hgc.jp/

转录因子预测软件：
March 1.0
http://compel.binet.nsc,ru/March/March.html
TFSEACH
http://www.cbrc.jp/research/db/TFSEACH.html
MAPPER
http://mapper.chip.org
P-March:
http://www.gene-regulation.com/pub/programs.html
TESS
http://www.cbil.upenn.edu/cgi-bin/tess/tess
PatSearch
http://www.ba.itb.cnr.it/BIG/PatSearch
m2transfac
http://explain.biobase.de/cgi-bin/m2transfac/bin/start.cgi
Signal Scan
http://www-bimas.cit.nih.gov/molbio/signal/
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4楼2014-08-13 00:08:50
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