Host &ndash Pathogen Protein Interactions Predicted by Structure
Introduction | Method | Predictions

Pathogen All predictions Filtered only  
Mycobacterium Mycobacterium tuberculosis  
Mycobacterium leprae
Kinetoplastida Leishmania major  
Trypanosoma brucei
Trypanosoma cruzi
Apicomplexa Cryptosporidium hominis  
Cryptosporidium parvum
Plasmodium falciparum
Plasmodium vivax
Toxoplasma gondii

Viewing the predictions

The All predictions files contain all interactions predictions for each species along with the filter criteria that each interaction passed. The Filtered only files contains the same information, but only for the subset of interactions that passed the biological and network-level filters. These files can be viewed in any spreadsheet program, such as Excel.

They can also be viewed in Cytoscape (at least ver 2.4): File → Import → Network from Table.

File format

The files are tab-delimited text files with the following columns:
  1. human_protein - protein identifier
  2. human_protein_descr - protein name
  3. pathogen_protein - protein identifier
  4. pathogen_protein_descr - protein name
  5. strx_PDB - PDB code of interaction template
  6. strx_tmpl1 - internal PIBASE identifier of domain 1
  7. strx_tmpl2 - internal PIBASE identifier of domain 2
  8. strx_zscore - statistical potential Z-score of predicted interaction
  9. seq_intact_id - IntAct identifier of interaction template
  10. seq_tmpl1 - protein identifier of host protein template
  11. seq_tmpl2 - protein identifier of pathogen protein template
  12. seq_joint_seqid - joint sequence identity
  13. netfilter - network filter status: "Fail" if the template has been used for more than 1% of the predictions in the species; otherwise "Pass"
  14. biofilter_h_num - Number of host biological criterion met
  15. biofilter_p_num - Number of pathogen biological criterion met
  16. biofilter_hp_num - Number of joint host-pathogen biological criterion met
  17. biofilter_h - Host biological criterion met
  18. biofilter_p - Pathogen biological criterion met
  19. biofilter_hp - Joint host-pathogen biological criterion met

We want to hear from you! Please send us any comments you have about the predictions.

questions: davisf at janelia dot hhmi dot org