Drug repurposing tools

Software Version Details Year
A Web Application for Predicting Drug Combination Efficacy Using Monotherapy Data and IDACombo A Web Application for Predicting Drug Combination Efficacy Using Monotherapy Data and IDACombo doi.org 2023
ACID ACID: a free tool for drug repurposing using consensus inverse docking strategy. doi.org 2019
ADEPTUS ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases. doi.org 2018
ASGARD ASGARD is A Single-cell Guided Pipeline to Aid Repurposing of Drugs doi.org 2023
Adera2.0 Adera2.0: A Drug Repurposing Workflow for Neuroimmunological Investigations Using Neural Networks. doi.org 2022
AlzGPS AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer’s drug discovery doi.org 2021
Anti-Dengue Anti-Dengue: A Machine Learning-Assisted Prediction of Small Molecule Antivirals against Dengue Virus and Implications in Drug Repurposing. doi.org 2023
AttentionSiteDTI AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification doi.org 2022
BALSAM Computational breath analysis exbio.wzw.tum.de NA
BGMSDDA BGMSDDA: a bipartite graph diffusion algorithm with multiple similarity integration for drug-disease association prediction. doi.org 2021
BiCoN Network-constrained biclustering of patients and omics data. doi.org 2021
BiRWDDA BiRWDDA: A Novel Drug Repositioning Method Based on Multisimilarity Fusion. doi.org 2019
BioProtIS BioProtIS: Streamlining protein-ligand interaction pipeline for analysis in genomic and transcriptomic exploration. doi.org 2024
CADDIE Cancer Driver Drug Interaction Explorer exbio.wzw.tum.de NA
CDPMF-DDA CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction doi.org 2025
CORDITE CORDITE: the curated CORona Drug InTERactions database for SARS-CoV-2 doi.org 2020
CPDR CPDR: An R Package of Recommending Personalized Drugs for Cancer Patients by Reversing the Individual’s Disease-Related Signature doi.org 2022
CPIExtract CPIExtract: A software package to collect and harmonize small molecule and protein interactions doi.org 2024
ChemBioServer 2.0 ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing doi.org 2020
ClustEval Large-scale clustering of big biomedical data sets github.com NA
Cmap CMap: Connectivity Map doi.org 2017
CoNVaQ Disease-specific copy number variation (CNV) identification exbio.wzw.tum.de NA
CoVex An interactive online platform for SARS-CoV-2 host interactome exploration and drug (target) identification. doi.org 2020
Cogena Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery doi.org 2016
Connectivity Map A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles science.org doi.org NA
CoryneRegNet CoryneRegNet is the international reference database for corynebacterial transcriptional gene regulatory interactions. exbio.wzw.tum.de NA
CovMulNet19 CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19 doi.org 2020
CytoGEDEVO Cytoscape implementation of the pairwise network alignment algorithm of GEDEVO apps.cytoscape.org NA
D3AI-CoV D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19 doi.org 2022
DDAPRED DDAPRED: a computational method for predicting drug repositioning using regularized logistic matrix factorization. doi.org 2020
DESMOND Identification of differentially expressed gene modules in heterogeneous diseases doi.org 2021
DESMOND2 Identification of differentially expressed gene modules in heterogeneous diseases github.com 2024
DIAMOnD A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome. doi.org 2015
DIGEST In silico validation of disease and gene sets, clusterings, or subnetworks digest-validation.net NA
DIGGER Exploring the functional role of alternative splicing in protein interactions doi.org 2021
DOMINO DOMINO: a network?based active module identification algorithm with reduced rate of false calls doi.org 2021
DOTA DOTA: Deep Learning Optimal Transport Approach to Advance Drug Repositioning for Alzheimer’s Disease doi.org 2022
DPDR-CPI DPDR-CPI, a server that predicts Drug Positioning and Drug Repositioning via Chemical-Protein Interactome doi.org 2016
DPNetinfer Pathway-Based Drug Repurposing with DPNetinfer: A Method to Predict Drug-Pathway Associations via Network-Based Approaches. doi.org 2021
DR2DI DR2DI: a powerful computational tool for predicting novel drug-disease associations doi.org 2018
DREBIOP DREBIOP: Drug REpurposing based on BIOlogical Pathways doi.org 2024
DREGE DREGE: Drug REpurposing based on GEnes doi.org 2024
DREIMT DREIMT: a drug repositioning database and prioritization tool for immunomodulation. doi.org 2021
DRIM DRIM: A Web-Based System for Investigating Drug Response at the Molecular Level by Condition-Specific Multi-Omics Data Integration doi.org 2020
DRIMC DRIMC: an improved drug repositioning approach using Bayesian inductive matrix completion doi.org 2020
DRviaSPCN DRviaSPCN: a software package for drug repurposing in cancer via a subpathway crosstalk network doi.org 2022
DTI-Voodoo DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions doi.org 2021
DTSEA DTSEA: Drug Target Set Enrichment Analysis method doi.org 2013
DTi2Vec DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning doi.org 2021
DTiGEMS+ DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques. doi.org 2020
DeSigN DeSigN: connecting gene expression with therapeutics for drug repurposing and development doi.org 2017
DeepACTION DeepACTION: A deep learning-based method for predicting novel drug-target interactions. doi.org 2020
DeepCLIP A context-aware neural network for modeling and predicting protein binding to nucleic acids using only sequence input. deepclip.compbio.sdu.dk NA
DeepDRK DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration. doi.org 2021
DeepMPF DeepMPF: deep learning framework for predicting drug–target interactions based on multi-modal representation with meta-path semantic analysis doi.org 2023
DeepSeq2Drug DeepSeq2Drug: An expandable ensemble end-to-end anti-viral drug repurposing benchmark framework by multi-modal embeddings and transfer learning. doi.org 2024
DeepsmirUD DeepsmirUD: Prediction of Regulatory Effects on microRNA Expression Mediated by Small Molecules Using Deep Learning. doi.org 2023
DenguePredict DenguePredict: An Integrated Drug Repositioning Approach towards Drug Discovery for Dengue. pmc.ncbi.nlm.nih.gov 2015
DiMmer EWAS data analysis - Detection of differentially methylated regions dimmer.compbio.sdu.dk NA
DiNiro Single-cell RNAseq data tool apps.cosy.bio NA
DrPOCS DrPOCS: Drug repositioning based on projection onto convex sets doi.org 2018
Drug ReposER Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning doi.org 2019
Drug2ways Drug2ways: Reasoning over causal paths in biological networks for drug discovery doi.org 2020
DrugGenEx-Net DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing doi.org 2016
DrugNet DrugNet: Network-based drug-disease prioritization by integrating heterogeneous data doi.org 2014
DrugPredict Using a novel computational drug-repositioning approach (DrugPredict) to rapidly identify potent drug candidates for cancer treatment doi.org 2018
DrugRep DrugRep: an automatic virtual screening server for drug repurposing doi.org 2023
DrugRepoBank DrugRepoBank: a comprehensive database and discovery platform for accelerating drug repositioning doi.org 2024
DrugSig DrugSig: A resource for computational drug repositioning utilizing gene expression signatures doi.org 2017
Drugst.One Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing doi.org 2024
DvD DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data doi.org 2013
EK-DRD EK-DRD: A Comprehensive Database for Drug Repositioning Inspired by Experimental Knowledge doi.org 2019
EMUDRA EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy. doi.org 2018
EhecRegNet EhecRegNet is a database of gene regulations conserved between E. coli K12 and human pathogenic EHEC strains. ehecregnet.compbio.sdu.dk NA
FeatureCloud an all-in-one platform to RUN, DEVELOP & PUBLISH federated & privacy-preserving machine learning algorithms. featurecloud.ai NA
Flimma Tool for differential gene expression analysis exbio.wzw.tum.de NA
GCMM GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing doi.org 2022
GEDEVO a method for pairwise network (graph) alignment gedevo.mpi-inf.mpg.de NA
GEDEVO-M an extension of GEDEVO for the alignment of multiple (>2) input networks. gedevo.mpi-inf.mpg.de NA
GIFDTI GIFDTI: Prediction of drug-target interactions based on global molecular and intermolecular interaction representation learning. doi.org 2022
GIPSy Bacterial genomic islands bioinformatics.org NA
GNBRs GNBRs: Global Network of Biomedical Relationships doi.org 2020
GPSnet A genome-wide positioning systems network algorithm for in silico drug repurposing doi.org 2019
GTEx GTEx: The Genotype-Tissue Expression project doi.org 2013
GUILDify v2.0 GUILDify v2.0: A tool to identify molecular networks underlying human diseases, their comorbidities and their druggable targets doi.org 2019
GrandForest An ensemble learning method for discovering disease-associated modules from genomic profiling data. exbio.wzw.tum.de NA
GraphSimViz Statistical quantification of association biases caused by disease definitions in network medicine graphsimviz.net NA
HeTDR HeTDR: Drug repositioning based on heterogeneous networks and text mining doi.org 2021
Heter-LP Heter-LP: A heterogeneous label propagation algorithm and its application in drug repositioning doi.org 2017
Hetionet An integrative network encoding knowledge from millions of biomedical studies. doi.org NA
HitSeekR High-throughput screening exbio.wzw.tum.de NA
Homopharma Homopharma: A new concept for exploring the molecular binding mechanisms and drug repurposing doi.org 2014
HyperAttentionDTI HyperAttentionDTI: improving drug-protein interaction prediction by sequence-based deep learning with attention mechanism doi.org 2022
IMSDB Computational breath analysis imsdb.mpi-inf.mpg.de NA
JAMI Java 8 tool for the fast computation of conditional mutual information from large datasets. github.com NA
KG-Predict KG-Predict: A knowledge graph computational framework for drug repurposing. doi.org 2022
KeyPathwayMiner a software for de novo network enrichment, aka network modules. exbio.wzw.tum.de NA
KeyPathwayMinerWeb Online multi-omics network enrichment doi.org 2016
MD-Miner MD-Miner: a network-based approach for personalized drug repositioning doi.org 2017
MGATRx MGATRx: Discovering Drug Repositioning Candidates Using Multi-View Graph Attention. doi.org 2022
MGNDTI MGNDTI: A Drug-Target Interaction Prediction Framework Based on Multimodal Representation Learning and the Gating Mechanism. doi.org 2024
MIRACLE Reverse phase protein array (RPPA) analysis github.com NA
MOKPE MOKPE: drug–target interaction prediction via manifold optimization based kernel preserving embedding doi.org 2023
MaizeStressDB robust data exploration tool tailored for the analysis of gene expression profiles in maize leaves apps.cosy.bio NA
Mantra 2.0 Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis doi.org 2014
Mdock MDock: A Suite for Molecular Inverse Docking and Target Prediction. doi.org 2021
MeSHDD MeSHDD: Literature-based drug-drug similarity for drug repositioning doi.org 2016
Mergeomics 2.0 Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics doi.org 2021
MetaPocket 2.0 Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. The web service of MetaPocket 2.0 and all the test datasets are freely available. doi.org 2011
NABEECO NABEECO solves network alignment using Bee Colony Optimization. nabeeco.mpi-inf.mpg.de NA
NEASE Network Enrichment method for Alternative Splicing Events github.com NA
NEUBOrg NEUBOrg: artificially induced whole-brain organoid platform doi.org 2021
NFFinder NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning doi.org 2015
NOD NOD: a web server to predict New use of Old Drugs to facilitate drug repurposing doi.org 2021
NOGEA NOGEA: A Network-oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning doi.org 2021
NTD-DR NTD-DR: Nonnegative tensor decomposition for drug repositioning doi.org 2022
NeDRex Network medicine for disease module identification and drug repurposing with the NeDRex platform doi.org 2021
NeoDTI NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions. doi.org 2019
NerLTR-DTA NerLTR-DTA: Drug-target binding affinity prediction based on neighbor relationship and learning to rank. doi.org 2022
Network-based prediction of drug combinations Network-based prediction of drug combinations doi.org 2019
Open MoA Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy doi.org 2023
OpenBioLink OpenBioLink: a benchmarking framework for large-scale biomedical link prediction. doi.org 2020
OpenLabFramework Laboratory managment and sample tracking github.com NA
PATHOME-Drug PATHOME-Drug: a subpathway-based poly-pharmacology drug-repositioning method. doi.org 2021
PIMD PIMD: An Integrative Approach for Drug Repositioning Using Multiple Characterization Fusion doi.org 2020
PIPS Bacterial genomic islands bioinformatics.org NA
PISTON PISTON: Predicting drug indications and side effects using topic modeling and natural language processing doi.org 2018
PROMISCUOUS 2.0 PROMISCUOUS 2.0: a resource for drug-repositioning doi.org 2021
PS4DR PS4DR: a multimodal workflow for identification and prioritization of drugs based on pathway signatures doi.org 2020
PT-Finder PT-Finder: A multi-modal neural network approach to target identification. doi.org 2024
Partea Privacy-Aware-Time-to-Event Analysis apps.cosy.bio NA
PathClass De novo pathway-based biomarker identification doi.org 2017
Pathway2Targets Pathway2Targets: an open-source pathway-based approach to repurpose therapeutic drugs and prioritize human targets doi.org 2023
PetriScape PetriScape is a tool for discrete Petri net simulation of biological networks in Cytoscape. apps.cytoscape.org NA
PharmacoNER Tagger PharmacoNER Tagger: a deep learning-based tool for automatically finding chemicals and drugs in Spanish medical texts doi.org 2019
PhenoPredict PhenoPredict: A disease phenome-wide drug repositioning approach towards schizophrenia drug discovery doi.org 2015
PocketDB An Augmented Pocketome: Detection and Analysis of Small-Molecule Binding Pockets in Proteins of Known 3D Structure doi.org 2018
PocketPipe A computational pipeline for integrated Pocketome prediction and comparison github.com 2019
PrankWeb A web server for ligand binding site prediction and visualization. doi.org 2019
PredictONCO PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning doi.org 2023
ProHarMeD Proteomic Meta-Study Harmonization, Mechanotyping and Drug-Repurposing Prediction apps.cosy.bio NA
ProphTools ProphTools: general prioritization tools for heterogeneous biological networks doi.org 2017
QUADrATiC QUADrATiC: scalable gene expression connectivity mapping for repurposing FDA-approved therapeutics doi.org 2016
RANKS RANKS: a flexible tool for node label ranking and classification in biological networks. doi.org 2016
RDKG-115 RDKG-115: Assisting drug repurposing and discovery for rare diseases by trimodal knowledge graph embedding doi.org 2023
RE:fine drugs’ RE:fine drugs’: an interactive dashboard to access drug repurposing opportunities doi.org 2016
ROBUST NA github.com NA
ROBUST-Web Online bias-aware disease module mining with ROBUST-Web robust-web.net NA
RepTB RepTB: a gene ontology based drug repurposing approach for tuberculosis doi.org 2018
RepurposeDrugs RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies doi.org 2024
RepurposeVS RepurposeVS: A Drug Repurposing-Focused Computational Method for Accurate Drug-Target Signature Predictions doi.org 2018
SANE SANE: A sequence combined attentive network embedding model for COVID-19 drug repositioning doi.org 2021
SAveRUNNER SAveRUNNER: an R-based tool for drug repurposing doi.org 2021
SCANet A workflow for single-cell co-expression based analysis github.com NA
SDTNBI SDTNBI: an integrated network and chemoinformatics tool for systematic prediction of drug-target interactions and drug repositioning. doi.org 2017
SNF-NN SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks doi.org 2021
SPIDR SPIDR: small-molecule peptide-influenced drug repurposing doi.org 2018
SPONGE Sparse Partial Correlations On Gene Expression bioconductor.org NA
Scellnetor clustering tool for scRNA-seq data that takes Scanpy generated AnnData objects in H5AD file-format as input. doi.org NA
SperoPredictor SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19 doi.org 2022
StackCPA StackCPA: A stacking model for compound-protein binding affinity prediction based on pocket multi-scale features doi.org 2023
StarGazer StarGazer: A Hybrid Intelligence Platform for Drug Target Prioritization and Digital Drug Repositioning Using Streamlit doi.org 2022
SuperPred 3.0 SuperPred 3.0: drug classification and target prediction—a machine learning approach doi.org 2022
TOPAS TOPAS, a network-based approach to detect disease modules in a top-down fashion doi.org 2022
Target Fisher Target Fisher: a Consensus Structure-Based Target Prediction Tool, and its Application in the Discovery of Selective MAO-B Inhibitors. doi.org 2024
TargetHunter TargetHunter: an in silico target identification tool for predicting therapeutic potential of small organic molecules based on chemogenomic database. doi.org 2013
TiCoNE a software for the analysis of time course expression data (e.g. gene expression) together with biological networks. apps.cytoscape.org NA
Transitivity Clustering Large-scale clustering of big biomedical data sets transclust.compbio.sdu.dk NA
UnPaSt UnPaSt is a novel method for identification of differentially expressed biclusters. github.com 2024
deepDR deepDR: a network-based deep learning approach to in silico drug repositioning doi.org 2019
drexml drexml: A command line tool and Python package for drug repurposing doi.org 2024
eMatchSite eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models doi.org 2014
gene2drug gene2drug: a computational tool for pathway-based rational drug repositioning doi.org 2018
iDOMO iDOMO: identification of drug combinations via multi-set operations for treating diseases doi.org 2025
iDrug iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding doi.org 2020
ksRepo ksRepo: a generalized platform for computational drug repositioning doi.org 2016
mediKanren The precision medicine process for treating rare disease using the artificial intelligence tool mediKanren doi.org 2022
sPLINK allows the federated, privacy-preserving analysis of genome-wide association studies (GWAS) data. exbio.wzw.tum.de NA
scDrug scDrug: From single-cell RNA-seq to drug response prediction doi.org 2022