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castlered木蟲 (小有名氣)
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[求助]
關(guān)于蛋白之間相互作用預(yù)測的問題
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我想看看一個(gè)基因有沒有可能是另一個(gè)基因的靶基因，有沒有預(yù)測這個(gè)的軟件或網(wǎng)站，比較容易操作的。非常感謝 |
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wizardfan: 金幣+2, 謝謝分享經(jīng)驗(yàn) 2013-10-24 07:24:32
感謝參與，應(yīng)助指數(shù) +1
wizardfan: 金幣+2, 謝謝分享經(jīng)驗(yàn) 2013-10-24 07:24:32
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用免費(fèi)軟件或者從免費(fèi)數(shù)據(jù)庫獲得配體多肽-受體蛋白質(zhì)的可能的相互作用的位點(diǎn)的序列信息。 （1）蛋白質(zhì)——蛋白質(zhì)相互作用位點(diǎn)預(yù)測 M. Michael Gromiha, Protein Bioinformatics——From sequence to Function, Elsevier, 2007, P258-P260.既可以通過氨基酸序列進(jìn)行預(yù)測，也可以通過蛋白質(zhì)的3D結(jié)構(gòu)加以預(yù)測。 （2） 根據(jù)Protein-protein interaction的“motif”在數(shù)據(jù)庫中搜索與多肽序列異相同或最接近的不同Protein中的motif接合的另一個(gè)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).” 引號(hào)內(nèi)的內(nèi)容摘自：Haian Fu edits, Protein-protein Interactions——Methods and Application, Human Press, 2004, P452-P454.圖在書上都有，引用此段內(nèi)容只是起到索引作用，具體內(nèi)容請(qǐng)查閱原書。 Scansite 網(wǎng)址： http://scansite.mit.edu/ 我試過，沒有問題，具體操作如果不愿意看以上引用內(nèi)容的英文原版書籍，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寫了用Scansite Motif (Sequence)去搜索對(duì)應(yīng)結(jié)合的蛋白質(zhì)，用受體蛋白質(zhì)去搜索其與配體結(jié)合位點(diǎn)的可能的氨基酸殘基的序列的操作方法。 （3）蛋白質(zhì)序列的基本性質(zhì)分析——氨基酸組成，分子質(zhì)量，等電點(diǎn)，親/疏水性，跨膜區(qū)，結(jié)構(gòu)功能域�！狿rot para tool. http://www.expasy.ch/tools/protparam.html. ---------李伍舉主編，計(jì)算機(jī)輔助分子生物學(xué)實(shí)驗(yàn)設(shè)計(jì)與分析，人民軍醫(yī)出版社，2009，P109-P114。 蛋白質(zhì)三級(jí)結(jié)構(gòu)結(jié)構(gòu)預(yù)測與顯示�！猄wissmodel: http://swissmodel.expasy.org/ →進(jìn)入命令界面。 --------李伍舉 主編，計(jì)算機(jī)輔助分子生物學(xué)實(shí)驗(yàn)設(shè)計(jì)與分析，人民軍醫(yī)出版社，2009，P162-P68。李伍舉 主編，計(jì)算機(jī)輔助分子生物學(xué)實(shí)驗(yàn)設(shè)計(jì)與分析，人民軍醫(yī)出版社，2009，主要是在寫李伍舉的實(shí)驗(yàn)室自己開發(fā)的biosun軟件，而沒有對(duì)于現(xiàn)在國際上流行的生物信息學(xué)軟件詳細(xì)介紹，所以李伍舉的書沒有多少價(jià)值。 基于同源建模預(yù)測蛋白質(zhì)的三級(jí)結(jié)構(gòu)的具體方法，請(qǐng)見： 岳俊杰、馮華、梁龍 主編，蛋白質(zhì)結(jié)構(gòu)預(yù)測實(shí)驗(yàn)指南，化學(xué)工業(yè)出版社，2010，P12-P31，該書內(nèi)容通俗易懂，內(nèi)容比較詳實(shí)，在中文版的蛋白質(zhì)結(jié)構(gòu)預(yù)測實(shí)驗(yàn)類可能算是寫得最好的了，當(dāng)然與英文版的蛋白質(zhì)結(jié)構(gòu)預(yù)測書籍沒有辦法相比。 （5）蛋白質(zhì)的功能位點(diǎn)預(yù)測——不一定能用到蛋白質(zhì)-蛋白質(zhì)，蛋白質(zhì)-多肽相互作用上，但至少能夠獲知蛋白質(zhì)的結(jié)構(gòu)域分布與分子表面位點(diǎn)，而且可能夠檢測出哪些domain/motif處于功能關(guān)鍵位點(diǎn)，在化學(xué)修飾時(shí)盡量避開。 執(zhí)行：基于網(wǎng)絡(luò)prosite數(shù)據(jù)庫的蛋白質(zhì)位點(diǎn)預(yù)測。 http://prosite.expasy.org/ |
2樓2013-10-23 11:27:28
3樓2013-11-28 18:51:47
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