Protein functional site prediction
Download
1 / 20

Protein Functional Site Prediction - PowerPoint PPT Presentation


  • 129 Views
  • Uploaded on

Protein Functional Site Prediction. The identification of protein regions responsible for stability and function is an especially important post-genomic problem

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Protein Functional Site Prediction' - hashim


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
Protein functional site prediction
Protein Functional Site Prediction

  • The identification of protein regions responsible for stability and function is an especially important post-genomic problem

  • With the explosion of genomic data from recent sequencing efforts, protein functional site prediction from only sequence is an increasingly important bioinformatic endeavor.


What is a functional site
What is a “Functional Site”?

  • Defining what constitutes a “functional site” is not trivial

  • Residues that include and cluster around known functionality are clear candidates for functional sites

  • We define a functional site as catalytic residues, binding sites, and regions that clustering around them.






Phylogenetic motifs
Phylogenetic motifs

  • PMs are short sequence fragments that conserve the overall familial phylogeny

  • Are they functional?

  • How do we detect them?


Phylogenetic motifs1
Phylogenetic motifs

  • PMs are short sequence fragments that conserve the overall familial phylogeny

  • Are they functional?

  • How do we detect them?

  • First we design a simple heuristic to find them

  • Then we see if the detected sites are functional


Phylogenetic motif identification
Phylogenetic Motif Identification

  • Compare all windowed trees with whole tree and keep track of the partition metric scores

  • Normalize all partition metric scores by calculating z-scores

  • Call these normalized scores Phylogenetic Similarity Z-scores (PSZ)

  • Set a PSZ threshold for identifying windows that represent phylogenetic motifs




TIM

Phylogenetic Similarity

False Positive Expectation


TIM

Phylogenetic Similarity

False Positive Expectation


Cytochrome p450
Cytochrome P450

Phylogenetic Similarity

False Positive Expectation


Cytochrome p4501
Cytochrome P450

Phylogenetic Similarity

False Positive Expectation


Enolase
Enolase

Phylogenetic Similarity

False Positive Expectation


Glycerol kinase
Glycerol Kinase

Phylogenetic Similarity

False Positive Expectation


Glycerol kinase1
Glycerol Kinase

Phylogenetic Similarity

False Positive Expectation


Myoglobin
Myoglobin

Phylogenetic Similarity

False Positive Expectation


Myoglobin1
Myoglobin

Phylogenetic Similarity

False Positive Expectation


ad