Metadata-Version: 2.1
Name: targetDB
Version: 1.3.1
Summary: Package with an application to generate report on potential drug targets
Home-page: https://github.com/sdecesco/targetDB
Author: Stephane De Cesco
Author-email: sdecesco@gmail.com
License: UNKNOWN
Description: TargetDB
        =========
        
        TargetDB 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 (using `fpocket`).
        
        **Tutorial**: A document containing details on the methods used can be found [HERE (pdf)](targetDB/resources/TargetDB_tutorial.pdf)
        
        Installation
        ------------
        ### Python package installation
        #### Pip installation
        
        ```
        pip install targetDB
        ```
        
        #### Conda installation
        
        ```
        conda create --name targetdb --channel bioconda targetdb
        conda activate targetdb
        target_DB --help
        ```
        
        ##### Python compatibility
        
        python version **>= 3.4**
        
        Preferred python distribution : [Anaconda 3](https://www.anaconda.com/download/)
        
        
        #### Database files installation
        
        This package relies on the use of sqlite database to properly function.
        
        ##### Required database
        
        + targetDB
        
        You can download a copy of the database [HERE](https://github.com/sdecesco/targetDB/releases/download/v1.3.1/TargetDB_20_12_19.db.zip)
        
        >This database contains all of the human genome genes that have a uniprot ID
        
        #### System compatibility
        
        + Linux
        + Windows
        + Mac (not tested)
        
        
        Usage
        -----
        targetDB package provides a user interface to use the tool: `targetDB`
        
        ### `targetDB`
        
        When using `targetDB` for the first time you will be asked to enter information about:
        + targetDB sqlite database file
        + path to save list output files
        + path to save detailed target output files
        + email address (used for pubmed searches if none provided no pubmed search will be run)
        
        Those informations will be stored in ~/.targetdb/config.ini
        
        ![Configuration panel](targetDB/resources/configuration.png)
        
        Once created it will automatically start the main user interface (as seen below)
        
        ![Main interface](targetDB/resources/targetdb_gui.png)
        
        
        Examples
        -----
        TargetDB can be used in three modes:
        + Single
        + List 
        + Spider plot 
        
        ####Single mode outputs
        A series of examples can be downloaded here (Excel file)
        + [ACHE](targetDB/examples/single_targets/ACHE_P22303.xlsx)
        + [APOE](targetDB/examples/single_targets/APOE_P02649.xlsx)
        + [BACE1](targetDB/examples/single_targets/BACE1_P56817.xlsx)
        + [Tau](targetDB/examples/single_targets/MAPT_P10636.xlsx)
        + [PSEN1](targetDB/examples/single_targets/PSEN1_P49768.xlsx)
        
        ####List mode outputs
        In this example we have used a list of 95 targets provided by the AMP-AD consortium ([LINK HERE](https://agora.ampadportal.org/genes/))
        
        You can download two version of the list with different weight used to construct the MPO Score
        + [AMPAD - Medicinal chemist pioritization](targetDB/examples/List_outputs/AMPAD_NomList_MedChemMPO.xlsx)
        + [AMPAD - Structural biologist pioritization](targetDB/examples/List_outputs/AMPAD_NomList_StructuralMPO.xlsx)
        
        You can also find a list used to prioritize an entire class of proteins (Solute Carrier Protein)
        + [SLC Prioritization](targetDB/examples/List_outputs/SLC_ListPrioritization.xlsx)
        
        A definition of all the columns in the output can also be downloaded
        + [Columns definition](targetDB/examples/List_outputs/TargetDB_list_output_columns_definition.xlsx)
        
        ####Spider Plots
        A spider plot is here used to quickly give an idea of the area in which a target has strength and weaknesses
        ![APOE](targetDB/resources/APOE_Spider.png)
        Here under a guide to help reading these plots: 
        ![Spider_guide](targetDB/resources/Figure_spider_plot_legend.png)
        
        Instructions to create a targetDB database from scratch
        ---
        >**`WARNING`**: This mode is not fully supported and we cannot guarantee it will execute without errors
        
        #### System compatibility
        + Linux
        
        ##### Database creation
        
        `target_DB`
        ![Database creation](targetDB/resources/target_DB_command.png)
        
        
        The list of required databases is :
        + ChEMBL v25
        
        ChEMBL sqlite database can be directly downloaded [HERE](https://www.ebi.ac.uk/chembl/downloads)
        
        >This mode will generate a targetDB database that can then be used in report mode
        
        #### Other dependencies for the database creation mode
        
        ##### blast
        This mode use blast locally to perform similarity search and sequence alignments
        
        information to download and install blast locally can be found [HERE](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
        
        ##### fpocket
        In order to perform binding pocket searches and assess their druggability the program fpocket is used
        
        >Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, "Fpocket: An open source platform for ligand pocket detection", BMC Bioinformatics, 2009, 10:168
        
        >Peter Schmidtke, Xavier Barril "Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites", J. Med. Chem., 2010, 53 (15), pp 5858â€“5867
        
        instructions to download and install fpocket can be found [HERE](https://github.com/Discngine/fpocket)
        
        Current version of targetDB works with fpocket3
        
        **targetDB will not be able to perform pocket search on windows as fpocket is not available on windows platform**
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3 :: Only
Description-Content-Type: text/markdown
