T. brucei query set (DSR VI/11/07)

Posted by David Roos on 2007-06-11 09:40:48

WARNING: This list was made prior to the version 4 release of TDR Targets (Aug, 2010). Some queries included in this list may not work properly. Most likely reasons for this are changes in parameters, and/or data updates. If you experience any problem, please try re-running each search from the search page.

List description

A set of attributes potentially relevant to T. brucei drug target design, including:
- enzymes [100]
- MW <100 kDa [20]
- no TM domains [20]
- structure available in PDB [50]
- model available in ModBase [30]
- present in all TriTryps [25]
- NOT in human [25]
- essentiality evidence in some (other) organism(s) [40]
- essential in T. brucei (lethal RNAi or KO phenotype) [50]
- druggability evidence inferred from orthology (>0.6) [35]
- compound desirability inferred from orthology (>0.3) [35]
- publications in PubMed [35]

Click on the links below to browse the contents of each query. You can also use the checkboxes to select queries you would like to import into your history.
Import ranked queries into your history to redo the scoring strategy
  • T. brucei targets - composite weighted query (DSR) (10965 records), 3
    • Score for genes in query #30 (Compound desirability (>0.3)): 35
    • Score for genes in query #27 (T. brucei <100kDa): 20
    • Score for genes in query #35 (T. brucei lethal (KO or KD)): 50
    • Score for genes in query #5 (Present in all TriTryps): 25
    • Score for genes in query #6 (T. brucei, NOT human): 25
    • Score for genes in query #34 (T. brucei published): 35
    • Score for genes in query #33 (T. brucei no TM domains): 20
    • Score for genes in query #4 (T. brucei models): 30
    • Score for genes in query #2 (T. brucei enzymes): 100
    • Score for genes in query #7 (Essential (in any organism)): 40
    • Score for genes in query #29 (Druggability precedent (>0.6)): 35
    • Score for genes in query #36 (T. brucei 3D structures): 50
  • T. brucei enzymes (776 records), 3
    • species: tbr
    • EC: any
  • T. brucei models (7119 records), 3
    • species: tbr
    • structures: Modbase
  • Present in all TriTryps (7332 records), 3
    • phylogenetic_distribution: IN tcr, IN lma
    • species: tbr
  • T. brucei, NOT human (5735 records), 3
    • species: tbr
    • phylogenetic_distribution: NOT IN hsa
  • Essential (in any organism) (1375 records), 3
    • essential: Any
    • species: tbr
  • T. brucei <100kDa (9913 records), 3
    • molecular_weight: < 100000
    • species: tbr
  • Druggability precedent (>0.6) (234 records), 3
    • species: tbr
    • druggability_index: > 0.6
  • Compound desirability (>0.3) (399 records), 3
    • compound_desirability_index: > 0.3
    • species: tbr
  • T. brucei no TM domains (9313 records), 3
    • tm_segments: < 1
    • species: tbr
  • T. brucei published (549 records), 3
    • pubmed: any
    • species: tbr
  • T. brucei lethal (KO or KD) (59 records), 3
    • species: tbr
    • phenotype: Q=PATO:0000718
  • T. brucei 3D structures (80 records), 3
    • structures: PDB
    • species: tbr