View source for KSH HW1 Protein analysis

<h2>&nbsp;Protein Pattern Analysis</h2>

<h2>Motif, Pattern, Profiling, Signature</h2>

<p>Sequence motif - amino acid sequence pattern that is widespread and has a biological significance</p>

<p>Cf)&nbsp;Structural motif - connectivity between&nbsp;secondary structure elements<sup>1) </sup>- The simplest structural motif is a helical bundle</p>

<p><a href="http://www.proteinstructures.com/Structure/Structure/protein-motifs_files/helix-bundle.jpg"><img alt="" src="http://www.proteinstructures.com/Structure/Structure/protein-motifs_files/helix-bundle.jpg" style="height:121px; width:161px" /></a>(<a href="http://www.proteinstructures.com/Structure/Structure/protein-motifs.html">http://www.proteinstructures.com/Structure/Structure/protein-motifs.html</a>)</p>

<p>Pattern - Characters that appear in common&nbsp;in one protein family</p>

<p>two or more patterns are associated with a single motif <sup>2)</sup></p>

<p>Protein Profiling - the detection of the character or quantity of specific sets of proteins</p>

<p>Signature - a part of whole pattern. Short diagnostic pattern that we can find the character of specific protein</p>

<h2>1. PROSITE (prosite.expasy.org)</h2>

<p><sup>3)</sup>A protein database which consists of the protein families, domains, functional sites, amino acid patterns and profiles.</p>

<p>They are manually curated by a team of Swiss Institute of Bioinformatics</p>

<h2>2. ISREC profile (bioinf.man.ac.uk/dbbrowser/bioactivity/newpfscan.html)</h2>

<p>&nbsp;</p>

<h2>3. BLOCKS (blocks.fhcrc.org)</h2>

<p>&nbsp;</p>

<h2>4. Pfam (pfam.xfam.ac.uk)</h2>

<p>&nbsp;</p>

<h2>5. PRINTS (bioinf.man.ac.uk/dbbrowser/PRINTS)</h2>

<p>&nbsp;</p>

<h3>6. Etc - PIR (pir.georgetown.edu/pirwww/index.shtml),</h3>

<h3>PSI-BLAST(blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE=Proteins&amp;PROGRAM=blastp&amp;RUN_PSIBLAST=on)</h3>

<p>To search similarity among amino acid sequences . PIR - Protein Informatics Resourse , PSI - Position Specific Iterated</p>

<hr />
<h2>&nbsp;Protein Structure Analysis</h2>

<h2>1. SWISS-MODEL (swissmodel.expasy.org)</h2>

<h2>2. CPHmodels (cbs.dtu.dk/services/CPHmodels)</h2>

<h2>3.&nbsp;CASP, Critical Assessment of Structure Prediction (predictioncenter.org)</h2>

<hr />
<h2>Example</h2>

<p>Human Serotonin Receptor</p>

<p>1. Search the amino acid sequence from NCBI</p>

<p><img alt="" src="/ckfinder/userfiles/images/Serotonin%20receptor_1.PNG" style="height:628px; width:883px" /></p>

<p>2. Get the FASTA format information from the sample</p>

<p><img alt="" src="/ckfinder/userfiles/images/Serotonin%20receptor_2.PNG" style="height:290px; width:508px" /></p>

<p>3. Do analysis using the analysis tools</p>

<p>&nbsp;</p>

<h3>Result</h3>

<p>1. Using CPHmodels</p>

<p><img alt="" src="/ckfinder/userfiles/images/Serotonin%20receptor_3.PNG" style="height:635px; width:1043px" /></p>

<p>&nbsp;</p>

<p>2. Using SWISS-MODELS<img alt="" src="/ckfinder/userfiles/images/Serotonin%20receptor_4.PNG" style="height:809px; width:1600px" /></p>

<p>Although the identity is not high (~ 40 %), they assumes&nbsp;the sample as a&nbsp;5&#39; hydroxytryptamine receptor. It is exactly&nbsp;&nbsp;correct because human serotonine receptor is known as 5&#39; hydroxytryptamin receptor<sup>4)</sup></p>

<p>&nbsp;</p>

<hr />
<h2>Reference</h2>

<p>*** All these websites are listed in the book called &#39;Bioinformatics with bioperl&#39; authored by Young-chang Kim</p>

<p>1) <a href="http://www.proteinstructures.com/Structure/Structure/protein-motifs.html">http://www.proteinstructures.com/Structure/Structure/protein-motifs.html</a></p>

<p>2) <a href="https://en.wikipedia.org/wiki/Sequence_motif">https://en.wikipedia.org/wiki/Sequence_motif</a></p>

<p>3) <a href="https://en.wikipedia.org/wiki/PROSITE">https://en.wikipedia.org/wiki/PROSITE</a></p>

<p>4) <a href="https://en.wikipedia.org/wiki/5-HT_receptor">https://en.wikipedia.org/wiki/5-HT_receptor</a></p>

<p>&nbsp;</p>

<p>[[Seung-hoon Kim]]</p>