Package: targetDB
TargetDBTargetDB is a tool to quickly query multiple publicly available databases and provide an integrated view of the information available about potential targets. A quick binding pocket search is also performed (usingfpocket).Tutorial: A document containing details on the methods used can be foundHERE (pdf)InstallationPython package installationPip installation (Preferred way)pip install targetDBInstallation will fail due to opentargets dependency - 08/11/2021(a fix will be needed and/or an opentarget-free version released)Conda installationconda create --name targetdb --channel bioconda targetdb
conda activate targetdb
target_DB --helpPython compatibilitypython version>= 3.4Preferred python distribution :Anaconda 3Database files installationThis package relies on the use of sqlite database to properly function.Required databasetargetDBYou can download a copy of the databaseHEREThis database contains all of the human genome genes that have a uniprot IDSystem compatibilityLinuxWindowsMac (not tested)UsagetargetDB package provides a user interface to use the tool:targetDBtargetDBWhen usingtargetDBfor the first time you will be asked to enter information about:targetDB sqlite database filepath to save list output filespath to save detailed target output filesemail address (used for pubmed searches if none provided no pubmed search will be run)Those informations will be stored in ~/.targetdb/config.iniOnce created it will automatically start the main user interface (as seen below)ExamplesTargetDB can be used in three modes:SingleListSpider plotSingle mode outputsA series of examples can be downloaded here (Excel file)ACHEAPOEBACE1TauPSEN1List mode outputsIn this example we have used a list of 95 targets provided by the AMP-AD consortium (LINK HERE)You can download two version of the list with different weight used to construct the MPO ScoreAMPAD - Medicinal chemist pioritizationAMPAD - Structural biologist pioritizationYou can also find a list used to prioritize an entire class of proteins (Solute Carrier Protein)SLC PrioritizationA definition of all the columns in the output can also be downloadedColumns definitionSpider PlotsA spider plot is here used to quickly give an idea of the area in which a target has strength and weaknessesHere under a guide to help reading these plots:Instructions to create a targetDB database from scratchWARNING: This mode is not fully supported and we cannot guarantee it will execute without errorsSystem compatibilityLinuxDatabase creationtarget_DBThe list of required databases is :ChEMBL v25ChEMBL sqlite database can be directly downloadedHEREThis mode will generate a targetDB database that can then be used in report modeOther dependencies for the database creation modeblastThis mode use blast locally to perform similarity search and sequence alignmentsinformation to download and install blast locally can be foundHEREfpocketIn order to perform binding pocket searches and assess their druggability the program fpocket is usedVincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, "Fpocket: An open source platform for ligand pocket detection", BMC Bioinformatics, 2009, 10:168Peter Schmidtke, Xavier Barril "Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites", J. Med. Chem., 2010, 53 (15), pp 5858–5867instructions to download and install fpocket can be foundHERECurrent version of targetDB works with fpocket3targetDB will not be able to perform pocket search on windows as fpocket is not available on windows platform