Current major release: 6 | Current minor release: 1
TDR Targets minor Release 6.1, April 2019
No major genome or chemical data updates in this minor release.
Expression datasets were integrated from a number of select organisms, and new expression queries were developed in this release for these cases.
Trypanosoma cruzi (Ribosome Profiling, Smircich P et al)
Plasmodium berghei (Gametocyte transcriptomics Yeoh et al, Global transcriptomics Otto T et al)
Plasmodium falciparum (Several studies, Zanghi et al, Otto TD et al, Lasonder et al)
Plasmodium vivax (Intraerythrocytic Transcriptome, Zhu L et al)
Entamoeba histolytica (Transcriptomics of virulent and avirulent strains, Hon CC et al)
Trypanosoma brucei (mRNA abundance, Siegel TN et al)
Leishmania major (Transcriptome profiling of human-infected macrophages, Fernandes MC et al)
Toxoplasma gondii (Several studies, Fritz HM et al, Sibley/Greg et al, Gregory et al)
Updated structural models for all Tier 1 Organisms in TDR Targets. Thanks to Ben Webb and Andrej Sali for their generous help in computing these!
Precomputed Network-Driven Prioritizations (NDPs) and
Network-Derived features (e.g. Druggability Scores) available for
all Tier 1 Organisms in TDR Targets. Target NDPs for each organism
are linked from the Data Summary page.
Also, NDPs for Orphan compounds are available for those organisms
for which there is phenotypic screening data in TDR Targets (also
linked from the Data Summary page).
As usual, we worked really hard debugging the code and query operations at the history so that everything works smoothly for you all!
If you happen to find an issue, let us know and we'll have it fixed ASAP
TDR Targets Major Release 6.0, August 2018
Multiple organisms have been added to the TDR Targets repository. Data for all other existing organisms were accordingly updated
Trypanosoma brucei gambiense
Loa Loa NEW!
Wolbachia Brugia malayi
Annotations were either calculated ad hoc using InterProScan v5.3, TMHMM v2.0, GPIPred and KAAS server; or directly extracted from corresponding upstream repositories for each organism.
Gene orthology was updated to OMCL v5.0
Drug repository was updated by implementing ChEMBL 23th release
Druggable targets were obtained by semi-automated curation of annotated bioactivities.
Added Toxoplasma gondii and Plasmodium berghei genome wide essentiality data. Also updated E. coli, C. elegans, S. cerevisiae essentiality data.
Major changes were made in the user interface to make it easier to use.
A set of priorization lists were made for Tier 1 pathogens for users to use a starting point for drug discovery projects.
A set of priorization lists were made for orphan compound sets from pathogen boxes for drug repositioning endeavors.
JME chemical drawing applet was replaced for Chemaxons Marvin JS application
The History section, which allows for query complex operations, has been refurbished and provides clearer clues on how the queries are going to be processed
The user may now peek into the network by visualizing targets and their neighbouring elements (wether this are annotations or compounds, or even related targets)
Predicted gene-drug interactions now rely ALSO in associations made through the network (view (2016) A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. Berenstein AJ, Magariños MP, Chernomoretz A, Agüero F. PLOS Neglected Tropical Diseases 10(1): e0004300.)
We worked really hard to deliver a bug free version to life. If you happen to find an issue, let us know and we'll have it fixed ASAP
TDR Targets Release 5, September 2011
Get lists of compounds associated with targets (and
viceversa). From the targets page, after querying the database and
obtaining a list of genes/targets it is now possible to obtain
the list of all/curated/predicted compounds. The mirror
operation is also available (from the compound search, get
Get orthologs (in a species of interest) from any list of
targets. For any query that retrieves a list of targets (e.g.
those with loss of fitness phenotypes in T. brucei) it is now
possible to get the corresponding list of orthologs (e.g. in T.
cruzi). This 'ortholog transformation' operation is available
from the history page.
Genome-wide essentiality data for T. brucei now available in
TDR Targets. Data from the paper by Alsford S et al (2011) was
integrated into TDR Targets, and is available for searches
either as phenotype descriptions (loss of fitness, gain of
fitness), or through the 'essentiality' searches (using
inference by orthology, and therefore allowing users to look for
e.g. 'T. cruzi genes with loss of fitness phenotypes in T.
brucei'. Data covers ~ 80% of the protein coding genes and
resulted in > 30,000 phenotype descriptions (including normal
Phenotype curation data is now available for T. cruzi. The
TDR Targets curation team completed an initial round of curation
for T. cruzi. Manually curated data is now available for 105 T.
cruzi genes, including the associations with 1174 compounds.
Additional information is now available for 3D Models.
Additional data contributed to TDR Targets by the Modbase team
at UCSF (Ursula Pieper, Andrej Sali) is now available for
evaluating the available structural models for each modelled
As usual there have been a number of bug fixes, the majority
of which were trivial or cosmetic. One important bug causing
problems with operations using prioritized lists at the history
page was fixed.
Warning! as for other releases, remember that items
saved in your history (saved queries) might now return a
different number of genes/compounds because of data updates. For
this release, expect all saved queries depending on T.
phenotypes to be outdated. Please re-run these queries to catch
up with the new data.
TDR Targets Release 4, June 2010
Chemical Compounds are now an integral part of the TDR
Targets database. Bioactive compounds from different upstream
sources (ChEMBL, DrugBank, PubChem) have been integrated into
the database. Their activities and
targets are shown. More information
about these new data can be found in the
Acknowledgements and Datasources page.
Orthology relationships between all gene products, and also
against protein targets in the ChEMBL database are now derived
from the OrthoMCL v4 database.
Genome data (gene models, annotation) have been updated and
synced to their corresponding upstream sources: Tuberculist
(http://tuberculist.epfl.ch, v2.3), Leprosy
(http://mycobrowser.epfl.ch, v2.1), GeneDB/TriTrypDB
(http://tritrypdb.org, v2.0), PlasmoDB (http://plasmodb.org,
v6.3), ToxoDB (http://toxodb.org, v6.0), GeneDB/SchistoDB
Pfam domains, and automated GO assignments (from InterPro);
and EC numbers and metabolic pathways (from KEGG), have been updated
New species have been added to the menu of species that are
available for phylogenetic queries: Apicomplexa: Babesia
bovis, several species of Cryptosporidium (hominis,
muris, neoformans, parvum), several additional species of
Plasmodium (berghei, chabaudi, knowlesi, yoelii), and
Neospora caninum; Kinetoplastida: several species of
Leishmania (braziliensis, infantum, mexicana), and
several species of Trypanosoma (brucei congolense, brucei
Curated phenotypes and drugs are now available for S. mansoni,
from the TDR Targets curation effort.
New functionality allows searches on chemical compounds.
This functionality allows both text based queries, as well as
queries that are started from molecules that are drawn by the
[Behind the scenes]
Improved and faster management of queries in the user
session (intersections, unions, re-weighting strategies)
Warnings: user data!
If you're a registered user of the database, and you have
stored (auto-saved or permanently saved) queries, in some
cases, these queries may display an incorrect number of genes;
and some queries may not work at all. These issues are caused
by data updates in TDR Targets, and can be easily solved by
re-running these queries again. Some affected queries are
those returning targets that belong to an ortholog group
(using an old OrthoMCL identifier, the query would fail to
retrieve targets in v4); and phylogenetic queries (due to the
update of the ortholog mappings queries may now return a
different number of genes).
TDR Targets Release 3, March 2009
3D models are now available at Modbase and have been
integrated for searching in TDR Targets for Schistosoma,
Brugia malayi, and its endosymbiont Wolbachia and M. leprae.
Contributed by Ursula Pieper and Andrej Sali (UCSF).
Pathways (1089 genes), EC numbers (637 genes) and updated
literature references for Brugia malayi.
Curated data on assays, and production of recombinant
proteins from BRENDA
Arabidopsis thaliana is now available in phylogenetic
queries as a representative of the Viridiplantae phylum. This
now allows searching for targets with/without orthologs in
Survey entries and references updated based on user input
it's now easier to revise the weighting/scoring strategy
of a ranked UNION.
it's now possible to run a prioritization session
(multi-step search) from the search page, without having to
see the results of each intermediate search query
support for user roles has been added (moderator, admin),
and an initial set of user input forms has been layed out
(comments associated with genes/targets, which moderators have
Links out to Tuberculist now go to their new site.
Lots of minor bugfixes and some other major (but too
TDR Targets Release 2, June 2008
Data & Features
Schistosoma mansoni. A new helminth genome has been
incorporated into TDR Targets. Version 4.0 of the S.
mansoni genome is now in TDR Targets.
New slideshow tutorials. Starting with this release we will be
providing short slideshow tutorials on different aspects of the site
functionality and/or usage.
Drug Targets Survey. In this release we have integrated the data
from the Human African Trypanosomiasis survey on drug targets. All entries
have been incorporated and linked to the corresponding targets and
New functional classification. genes have been classified in
three main categories (enzymes, receptors, transporters). This manual
classification (described in the documentation) complements the other
classification schemes available (metabolic pathways, GO slims), providing
more search options.
Query history page. You can now export smarter spreadsheets that
will allow you to re-prioritize datasets on the fly by changing weights to
each criteria. There is also a new interface for easier subtraction between
queries, and other minor changes to the history UI we expect will make your
More PDB structures for Mycobacterium tuberculosis. We have
updated the list of PDB structures available for M. tuberculosis.
All these structures are also available for M. leprae.
Curated target information for M. tuberculosis
and M. leprae. As part of the ongoing curation
effort, we have loaded curated information for M. tuberculosis.
Result tables. You can now re-sort the results of queries, and
also specify the number of records that should be displayed per page.
Bugfixes. Lots of bugfixes are included in this release. Keep
sending your bug reports!
TDR Targets Release 1, April 2007
Data & Features
Presentation of TDR Targets. TDR Targets was unveiled on April
16th in Geneva at a meeting of TDR's Drug Discovery committee.
First genomes. The first genomes included in TDR Targets are
those of: Plasmodium falciparum, Mycobacterium tuberculosis, Trypanosoma
brucei, Leishmania major and Trypanosoma cruzi.