You'r here:Results
Characterizing the pocketome of Mycobacterium tuberculosis and rationalization of polypharmacological target selection.
Mapping the small molecule binding pocket space in Mtb: Characterization of the MtbPocketome
Following files contain the information on the tripartite network constructure between protein-ligand associations obtained from kegg, chemical similarity associations obtained between KEGG ligands and PDB ligands, and finally protein-ligand association obtained for chemically similar ligands in PDB through PocketMatch.
- Rvprotein_keggligand_associations.txt - This file contains information about Mtb protein and corresponding KEGG ligand associations obtained from KEGG database.
- Rvprotein_PDBLigand_associations.txt - This file contains associations of Mtb proteins with the ligands from PDB.
- KEGGCID_PDBLigand_associations.txt - This file contains the information on mapping KEGG ligand to PDB hetatm mapping obtained through tanimoto chemical similarity.
- Mtb_proteins_Ligand_association_PMScores.csv - This file contains all the ligand associations of Mtb proteins along with the information of the pocket that has matched and PocketMatch Scores obtained from Procognate database comparison.
- MtbPocketome_topmostPDBLig_hits.txt - This file contains the information on topmost ligand hit found from PDB for each of the sites using PocketMatch.
Binding site space of Mtb proteome is much higher than the sequence or the fold space
Following files contains the supporting information on binding site space and the sequence-structure-pocket relationship.
- Sequence_Structure_PocketSimilarity.csv - This file contains information on all sequence-structure-function relationship.
- MtbPocketpairs_above60PMAX.txt - This file contains information on all the pocket-pairs within Mtb having similarity above 0.60 PMAX.
Identifying polypharmacological target sets from Mtb binding site similarity network
All the supporting files for obtaining the polypharmacological sets from sequence,structure and pocket similarity is given in these files.
- SequenceSim_MCODE_Results.txt - This file contains the information on sequence clusters in Mtb that are paralogous to each other.
- StructureSim_MCODE_Results.txt - This file contains the information on structure clusters in Mtb that are highly similar. (Hence could share similar pockets too.)
- PocketsSim_MCODE_Results.txt - This file contains information on pocket clusters obtained for similar sites at PMAX 0.6 cut-off.
- Mtb_within_significant_hits.csv - This file contains the information of significant similarity hits found within Mtb pocketome.
- MCODE_Mtbpocketome_results.txt - This file contains the MCODE clustering results for MtbPocketome.
- Mtb_PocketomeSet_enrichment_analysis.zip - This zip file contains the enrichment analysis carried out for the set of similar binding sites.
- Binding_site_Set_Alignment.zip - This zip file contains the pymol session file displaying all alignment of binding sites within the set.
Comparison of Mtbpocketome with known drug-binding sites
These files contain the information on drug associations obtained through comparison of drug binding sites obtained from drugbank.
- MtbPocketome_Drugbank_hits_PMAX60.txt - This file contains the information on the all the drugbank hits obtained for each of the binding site sets.
- All_set_drugbank_hit_frequency.csv - This file contains the frequency hits of each of the drugs within the sets and excludes the co-factor.
- TableS5
Clues for drug-repurposing
These files contain the supporting information on the associations obtained between high-confidence targets from targetTB and approved drugs through binding site comparison using PocketMatch algorithm.
- Protein_drug_association.tsv - This csv file contains the information on drug association for protein pockets within Mtb.
- Drug-target_graph.cys - This file is the cytoscape session of drug-target network in this study. Please follow this link: http://wiki.cytoscape.org/GettingStarted for downloading Cytoscape and opening the session file.
- Targets_description.xlsx - This microsoft excel file contains the information of targets present in the network, prioritized according to their clustering-coefficient in the network.
- Drug_repurposing.xlsx - This microsoft excel file contains the information of drugs that could have potential of repurposing for antimycobacterial activity, prioritized according to clustering coefficient in drug-target network.
