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Protein function from its emergence to diversity in contemporary proteins

Online Supplementary Materials and scripts for the Physical Biology paper on proteins and their elementary functions

Contents:

  1. Input data files

  2. Python script to reproduce the results

  3. Sample output files used to create the graphs

  4. Graphs as cytoscape sessions

  5. Copies of graphs in HTML format

Figure 2: http://169.228.38.217:3000/#/https%253A%252F%252Fraw.githubusercontent.com%252Fneksa%252Felementary-functions%252Fmaster%252FCytoscape%252FFigure2.json?stylefile=https:%2F%2Fraw.githubusercontent.com%2Fneksa%2Felementary-functions%2Fmaster%2FCytoscape%2Fstyle.json&selectedstyle=EF

Figure 3: http://169.228.38.217:3000/#/https%253A%252F%252Fraw.githubusercontent.com%252Fneksa%252Felementary-functions%252Fmaster%252FCytoscape%252FFigure3.json?stylefile=https:%2F%2Fraw.githubusercontent.com%2Fneksa%2Felementary-functions%2Fmaster%2FCytoscape%2Fstyle.json&selectedstyle=EF

Figure 4: http://169.228.38.217:3000/#/https%253A%252F%252Fraw.githubusercontent.com%252Fneksa%252Felementary-functions%252Fmaster%252FCytoscape%252FFigure4.json?stylefile=https:%2F%2Fraw.githubusercontent.com%2Fneksa%2Felementary-functions%2Fmaster%2FCytoscape%2Fstyle.json&selectedstyle=EF

Figure 5: http://169.228.38.217:3000/#/https%253A%252F%252Fraw.githubusercontent.com%252Fneksa%252Felementary-functions%252Fmaster%252FCytoscape%252FFigure5.json?stylefile=https:%2F%2Fraw.githubusercontent.com%2Fneksa%2Felementary-functions%2Fmaster%2FCytoscape%2Fstyle.json&selectedstyle=EF

  1. Compositonal statistics of active/catalytic sites and their sizes in CSA and CDD

Combinatorial statistics of the active sites in CSA

Literature annotated sites:

Total: 558 1 Total monads: 14 2 Total dyads: 68 3 Total triads: 144 4 Total tetrads: 145 5 Total pentads: 94 6 Total hexads: 56 7 Total heptads: 17

Literature and PSI-BLAST annotated sites:

Total: 1753 1 Total monads: 20 2 Total dyads: 149 3 Total triads: 393 4 Total tetrads: 424 5 Total pentads: 304 6 Total hexads: 230 7 Total heptads: 92