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The Protein Feature View

Build Status

SVG library for visualising protein annotations

This is the library behind the Protein Feature View at RCSB PDB.

Screenshot of Protein Feature View at RCSB

Legend

The Protein Feature View requires a browser that supports SVG (Scalable Vector Graphics). Mouse over tracks and labels for more information.

Data origin/color codes

The vertical color bar on the left side indicates data provenance.

Data in green originates from UniProtKB

Data in yellow originates from Pfam, by interacting with the HMMER3 web site
Data in purple originates from Phosphosite.
Data in orange originates from the SCOP (version 1.75) and SCOPe (version 2.04) classifications.
Data in grey has been calculated using BioJava  . Protein disorder predictions are based on JRONN (Troshin, P. and Barton, G. J. unpublished), a Java implementation of RONN   
<ul>
  <li>
    Red: potentially disorderd region
  </li>

  <li> Blue: probably ordered region.
  </li>
</ul>

Hydropathy has been calculated using a sliding window of 15 residues and summing up scores from standard hydrophobicity tables.

  • Red: hydrophobic
  • Blue: hydrophilic.

Data in lilac represent the genomic exon structure projected onto the UniProt sequence.

Data in blue originates from PDB

  • Secstruc: Secondary structure projected from representative PDB entries onto the UniProt sequence.

Data in red indicates combined ranges of Homology Models from SBKB   and the Protein Model Portal  

Event model

An event model allows to register "listeners" that get triggered when certain events occur. A listener can get registered with:

 pfv.addListener(eventName,function);

currently supported events:

  • viewerReady
  • sliderMoved
  • sliderReleased

Dependencies

  • jquery (V. 1.7.2+)
  • jquery SVG (V. 1.4.5+)
  • bootstrap-slider (V. 4.10.0+)

License

GPL 3.0 http://www.gnu.org/licenses/gpl.html

How to cite

At the present, there is no primary citation yet, however Protein Feature View got mentioned in the most recent RCSB PDB Nucleic acid research database issue paper.

Author

Andreas Prlic - RCSB Protein Data Bank

How to get started?

Take a look at minimal.html for how to create a basic setup