Difference between revisions of "KSH HW1 Protein analysis"
imported>Seung-hoon Kim |
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<h2> Protein Pattern Analysis</h2> | <h2> Protein Pattern Analysis</h2> | ||
| − | <h2>Motif, Pattern, | + | <h2>Motif, Pattern, Profiling, Signature</h2> |
| − | <p> </p> | + | <p>Sequence motif - amino acid sequence pattern that is widespread and has a biological significance</p> |
| + | |||
| + | <p>Cf) Structural motif - connectivity between 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 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> | <h2>1. PROSITE (prosite.expasy.org)</h2> | ||
| − | <p><sup> | + | <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> | <p>They are manually curated by a team of Swiss Institute of Bioinformatics</p> | ||
| Line 38: | Line 50: | ||
<h2>1. SWISS-MODEL (swissmodel.expasy.org)</h2> | <h2>1. SWISS-MODEL (swissmodel.expasy.org)</h2> | ||
| − | <h2>2. CPHmodels</h2> | + | <h2>2. CPHmodels (cbs.dtu.dk/services/CPHmodels)</h2> |
<h2>3. CASP, Critical Assessment of Structure Prediction (predictioncenter.org)</h2> | <h2>3. 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> </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> </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 the sample as a 5' hydroxytryptamine receptor. It is exactly correct because human serotonine receptor is known as 5' hydroxytryptamin receptor<sup>4)</sup></p> | ||
| + | |||
| + | <p> </p> | ||
| + | |||
| + | <hr /> | ||
<h2>Reference</h2> | <h2>Reference</h2> | ||
<p>*** All these websites are listed in the book called 'Bioinformatics with bioperl' authored by Young-chang Kim</p> | <p>*** All these websites are listed in the book called 'Bioinformatics with bioperl' authored by Young-chang Kim</p> | ||
| − | <p>1) <a href=" | + | <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> | + | <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> </p> | <p> </p> | ||
<p>[[Seung-hoon Kim]]</p> | <p>[[Seung-hoon Kim]]</p> | ||
Latest revision as of 00:02, 18 June 2016
Contents
- 1 Protein Pattern Analysis
- 2 Motif, Pattern, Profiling, Signature
- 3 1. PROSITE (prosite.expasy.org)
- 4 2. ISREC profile (bioinf.man.ac.uk/dbbrowser/bioactivity/newpfscan.html)
- 5 3. BLOCKS (blocks.fhcrc.org)
- 6 4. Pfam (pfam.xfam.ac.uk)
- 7 5. PRINTS (bioinf.man.ac.uk/dbbrowser/PRINTS)
- 8 Protein Structure Analysis
- 9 1. SWISS-MODEL (swissmodel.expasy.org)
- 10 2. CPHmodels (cbs.dtu.dk/services/CPHmodels)
- 11 3. CASP, Critical Assessment of Structure Prediction (predictioncenter.org)
- 12 Example
- 13 Reference
Protein Pattern Analysis
Motif, Pattern, Profiling, Signature
Sequence motif - amino acid sequence pattern that is widespread and has a biological significance
Cf) Structural motif - connectivity between secondary structure elements1) - The simplest structural motif is a helical bundle
(http://www.proteinstructures.com/Structure/Structure/protein-motifs.html)
Pattern - Characters that appear in common in one protein family
two or more patterns are associated with a single motif 2)
Protein Profiling - the detection of the character or quantity of specific sets of proteins
Signature - a part of whole pattern. Short diagnostic pattern that we can find the character of specific protein
1. PROSITE (prosite.expasy.org)
3)A protein database which consists of the protein families, domains, functional sites, amino acid patterns and profiles.
They are manually curated by a team of Swiss Institute of Bioinformatics
2. ISREC profile (bioinf.man.ac.uk/dbbrowser/bioactivity/newpfscan.html)
3. BLOCKS (blocks.fhcrc.org)
4. Pfam (pfam.xfam.ac.uk)
5. PRINTS (bioinf.man.ac.uk/dbbrowser/PRINTS)
6. Etc - PIR (pir.georgetown.edu/pirwww/index.shtml),
PSI-BLAST(blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on)
To search similarity among amino acid sequences . PIR - Protein Informatics Resourse , PSI - Position Specific Iterated
Protein Structure Analysis
1. SWISS-MODEL (swissmodel.expasy.org)
2. CPHmodels (cbs.dtu.dk/services/CPHmodels)
3. CASP, Critical Assessment of Structure Prediction (predictioncenter.org)
Example
Human Serotonin Receptor
1. Search the amino acid sequence from NCBI
2. Get the FASTA format information from the sample
3. Do analysis using the analysis tools
Result
1. Using CPHmodels
2. Using SWISS-MODELS
Although the identity is not high (~ 40 %), they assumes the sample as a 5' hydroxytryptamine receptor. It is exactly correct because human serotonine receptor is known as 5' hydroxytryptamin receptor4)
Reference
*** All these websites are listed in the book called 'Bioinformatics with bioperl' authored by Young-chang Kim
1) http://www.proteinstructures.com/Structure/Structure/protein-motifs.html
2) https://en.wikipedia.org/wiki/Sequence_motif
3) https://en.wikipedia.org/wiki/PROSITE
4) https://en.wikipedia.org/wiki/5-HT_receptor
