Supplementary Material for "Global View of the Protein Universe"

Supplementary Material for "A Global View of the Protein Universe" by Nepomnyachiy, Ben-Tal, Kolodny.

If you encounter a problem, Email us:
Sergey Nepomnyachiy (nsergey82 at gmail dot com), Nir Ben-Tal (bental at tauex dot tau dot ac dot il), Rachel Kolodny (trachel at cs dot haifa dot ac dot il).

Initial steps:

(1) Install Cytoscape (download version >3.x here)

(2) Install PyMOL (version 1.3 or newer)

(3) Add the the pymol executable to the Path. Here are detailed instructions for Windows

(4) Download our data file, and unzip it

(5) Install our CyToScape app: Here are detailed instructions. CyToStruct code and demos can be found Here

Viewing the domain network:

(6) Double-click on the file df_domains.cys, in the directory you just downloaded.

(7) To view a domain: right click on a node, and use CyToStruct->open in PyMOL

(8) To view a motif: right click on an edge, and use CyToStruct->open in PyMOL

Viewing the motif network:

(9) Double-click on the file df_motifs.cys, in the directory you just downloaded

(10) To view a motif: right click on a node, and use CyToStruct->open in PyMOL

(11) To view a domain that connects two motifs: right click on an edge, and use CyToStruct->open in PyMOL