Table 5.
Web-tools and open source kits.
| Tool | Description | URL | Ref |
|---|---|---|---|
| Clue | Tools for perturbagens (small molecules or genes) query, L1000 cohorts, and gene expression heatmap visualization | https://clue.io | [44] |
| Clue Repurposing Tool | Interactive application to access approved and pre-clinical drug annotations | https://clue.io/repurposing | [137] |
| COGENA | Analysis, visualizing and clustering tool for gene expression profiles | https://github.com/zhilongjia/cogena | [138] |
| DeepChem | Deep learning toolkit for drug discovery and cheminformatics | https://deepchem.io/ | [139] |
| DR.PRODIS | Prediction of drug-protein interactions, side effects | http://cssb.biology.gatech.edu/repurpose | [140] |
| e-LEA3D | Collection of tools related to computer-aided drug design | http://chemoinfo.ipmc.cnrs.fr/ | [141] |
| Frog2 | Chemo-informatics toolkit for small compound 3D generation from 1D/2D input | http://bioserv.rpbs.univ-paris-diderot.fr/services/Frog2/ | [142] |
| GIFT | Infer chemogenomic features from drug-target interactions. | http://bioinfo.au.tsinghua.edu.cn/software/GIFT/ | [143] |
| GoPredict | Drug target prioritization tool for breast and ovarian cancer | http://csblcanges.fimm.fi/GOPredict/ | [144] |
| JOELib/JOELib2 | Toolkit to interconvert chemical file formats, descriptor calculation classes, and SMARTS substructure search | http://www.ra.cs.uni-tuebingen.de/software/joelib/introduction.html | [145] |
| ksRepo | Drug repositioning tool that utilizes gene expression drug datasets from different platforms | https://github.com/adam-sam-brown/ksRepo | [101] |
| L1000CDS | L1000 dataset based gene expression signature search engine | http://amp.pharm.mssm.edu/L1000CDS2/#/index | [146] |
| MANTRA | Prediction and analysis of mechanism of action of drugs for drug repositioning | http://mantra.tigem.it/ | [147] |
| NFFinder | Tool to discover multiple drugs with similar drugs based on up/down regulated genes | http://nffinder.cnb.csic.es/ | [102] |
| Open babel | Open source chemistry toolbox | http://openbabel.org/wiki/Main_Page | [148] |
| Open PHACTS | European funded initiative to bring together industry and academic partners for semantic integration of pharmacological data using an RDF data model | http://www.openphacts.org | [149] |