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castlered木虫 (小有名气)
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[求助]
关于蛋白之间相互作用预测的问题
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我想看看一个基因有没有可能是另一个基因的靶基因，有没有预测这个的软件或网站，比较容易操作的。非常感谢 |
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凌波丽
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【答案】应助回帖
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感谢参与，应助指数 +1
wizardfan: 金币+2, 谢谢分享经验 2013-10-24 07:24:32
感谢参与，应助指数 +1
wizardfan: 金币+2, 谢谢分享经验 2013-10-24 07:24:32
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用免费软件或者从免费数据库获得配体多肽-受体蛋白质的可能的相互作用的位点的序列信息。 （1）蛋白质——蛋白质相互作用位点预测 M. Michael Gromiha, Protein Bioinformatics——From sequence to Function, Elsevier, 2007, P258-P260.既可以通过氨基酸序列进行预测，也可以通过蛋白质的3D结构加以预测。 （2） 根据Protein-protein interaction的“motif”在数据库中搜索与多肽序列异相同或最接近的不同Protein中的motif接合的另一个Protein的motif。 Motif scan of a protein from a public database. ——Haian Fu edits, Protein-protein Interactions——Methods and Application, Human Press, 2004, P445-P465. “Motif Scan of a Protein from a Public Database This program will scan one protein for all of the motifs in Scansite (or a subset of them, at your choosing). In a web browser, go to the URL http://scansite.mit.edu.You will see the Scansite home page as shown in Fig. 1. 2. Under the “Motif Scan” heading, click “Scan a Protein by Accession Number or ID.” 3. Enter the accession number or ID in the text field labeled “Protein ID or Accession Number” (see Note 1). 4. Select which public database you will be accessing (Swiss-Prot, TrEMBL, Genpept, or Ensembl) from the drop-down box. 5. Choose which motifs in Scansite’s database to scan. To scan for all motifs, click the checkbox labeled “Look for all motifs.” To scan only for motifs you specify, click the checkbox labeled “Look only for motifs and groups selected below.” Select one or more items in the “Individual Motifs” list, and/or one or more items in the “Motif Groups” list. 6. Choose the stringency level desired: high, medium, or low. This sets how high a sequence must score to be reported. These thresholds are set based on the scores of all subsequences that match the motif within the entire vertebrate collection of Swiss-Prot proteins. High stringency indicates that the motif identified in the query sequence is within the top 0.2% of all matching sequences contained in vertebrate Swiss-Prot proteins. Medium and low stringency scores correspond to the top 1% and 5% of sequence matches, respectively. Sites identified under highstringency scoring are likely to be correct, although there is a possibility that real sites will fail to be identified (i.e., a nonzero false-negative selection rate). In contrast, medium and low stringency scoring has a much lower rate of falsenegative predictions, but tends to over-call motif sites, resulting in increasing numbers of false-positive hits (see Note 2). 7. To show domains recognized in your sequence, check the box labeled “Show predicted domains in sequence.” Otherwise, uncheck it. 8. Click “Submit Request” (see Note 3). Figure 2 shows an example of the output. Your protein is drawn as a thin rectangle. If any sites were found, they are marked above the rectangle with a short-hand name of the domain type (such as “Y_Kin,” “SH2,” or “PDZ”). If you requested the domains in your sequence to be shown, they will be marked as colored boxes with their names and residue ranges annotated below the rectangle. If phosphorylation and domain-binding sites already known from the literature are present, these will be marked below the domain names in a row labeled “Mapped sites” (none are present in this example). Further down, a plot of the surface accessibility indicates residues that are likely to be near the protein surface and thus able to interact with other proteins. At the bottom, a simple ruler indicates every hundredth position in the input protein sequence.Below the protein image is a table listing the details of the sites found (see Fig. 3). Similar motifs are grouped together (for example, all tyrosine-kinase domains). The table indicates the motif name and Gene Card (if one exists) for each site found. The next line lists each site found for that motif, with its score, the percentile that protein’s score falls into compared with all vertebrate proteins in Swiss-Prot, the sequence surrounding that site, and the solvent accessibility at that position. Clicking on the Gene Card takes you to that entry on the Gene Card site (25). Clicking on the near-site sequence displays the full protein sequence with the site location highlighted. Clicking on the score displays a histogram showing where this score falls in the distribution of all vertebrate Swiss-Prot proteins that have been scored for this motif (see Note 4).” 引号内的内容摘自：Haian Fu edits, Protein-protein Interactions——Methods and Application, Human Press, 2004, P452-P454.图在书上都有，引用此段内容只是起到索引作用，具体内容请查阅原书。 Scansite 网址： http://scansite.mit.edu/ 我试过，没有问题，具体操作如果不愿意看以上引用内容的英文原版书籍，也可以看Haian Fu edits, Protein-protein Interactions——Methods and Application, Human Press, 2004, 的中文版。 在Haian Fu edits, Protein-Protein Interactions——Methods and Application, Human Press, 2004, P445-P467写了用Scansite Motif (Sequence)去搜索对应结合的蛋白质，用受体蛋白质去搜索其与配体结合位点的可能的氨基酸残基的序列的操作方法。 （3）蛋白质序列的基本性质分析——氨基酸组成，分子质量，等电点，亲/疏水性，跨膜区，结构功能域。——Prot para tool. http://www.expasy.ch/tools/protparam.html. ---------李伍举主编，计算机辅助分子生物学实验设计与分析，人民军医出版社，2009，P109-P114。 蛋白质三级结构结构预测与显示。——Swissmodel: http://swissmodel.expasy.org/ →进入命令界面。 --------李伍举 主编，计算机辅助分子生物学实验设计与分析，人民军医出版社，2009，P162-P68。李伍举 主编，计算机辅助分子生物学实验设计与分析，人民军医出版社，2009，主要是在写李伍举的实验室自己开发的biosun软件，而没有对于现在国际上流行的生物信息学软件详细介绍，所以李伍举的书没有多少价值。 基于同源建模预测蛋白质的三级结构的具体方法，请见： 岳俊杰、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，P12-P31，该书内容通俗易懂，内容比较详实，在中文版的蛋白质结构预测实验类可能算是写得最好的了，当然与英文版的蛋白质结构预测书籍没有办法相比。 （5）蛋白质的功能位点预测——不一定能用到蛋白质-蛋白质，蛋白质-多肽相互作用上，但至少能够获知蛋白质的结构域分布与分子表面位点，而且可能够检测出哪些domain/motif处于功能关键位点，在化学修饰时尽量避开。 执行：基于网络prosite数据库的蛋白质位点预测。 http://prosite.expasy.org/ |
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