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Drug repurposing tools

Drug repositioning has been regarded as one of the most promising strategies for translational medicine. Common efforts to find new uses for existing drugs depend on text mining (Andronis et al., 2011), chemical genetics (Iorio et al., 2010) and…
PASS
Desktop

PASS Prediction of Activity Spectra for Substances

Predicts many kinds of biological activity for compounds from different…

Predicts many kinds of biological activity for compounds from different chemical series based on their 2D structural formulas. PASS finds new targets mechanisms for some ligands. It can reveal new…

PROMISCUOUS
Dataset

PROMISCUOUS

An exhaustive resource of protein-protein and drug-protein interactions with…

An exhaustive resource of protein-protein and drug-protein interactions with the aim of providing a uniform data set for drug repositioning and further analysis.

eMolFrag
Desktop

eMolFrag

Extracts molecular fragments, classified as bricks and linkers, from small…

Extracts molecular fragments, classified as bricks and linkers, from small molecule datasets. eMolFrag uses the fragments in order to construct targeted libraries for virtual screening. It stores the…

REMAP
Desktop

REMAP

A dual-regularized one class collaborative filtering algorithm for biological…

A dual-regularized one class collaborative filtering algorithm for biological relation prediction. REMAP explores continuous chemical space, protein space, and their interactome on a large scale.…

GeneDiseaseRepo…
Desktop

GeneDiseaseRepositioning

An integrated data driven approach to drug repositioning.…

An integrated data driven approach to drug repositioning. GeneDiseaseRepositioning is an exhaustive approach for identifying new uses for existing drugs, with a focus on gene-disease (G-D)…

LRSSL
Desktop

LRSSL Laplacian regularized sparse subspace learning

Predicts and interprets drug–disease associations of new drugs and approved…

Predicts and interprets drug–disease associations of new drugs and approved drugs. LRSSL integrates drug chemical information, drug target domain information and target annotation information. It…

MANTRA
Web

MANTRA Mode of Action by NeTwoRk Analysis

Allows to analyze the Mode of Action (MoA) of novel drugs and to identify known…

Allows to analyze the Mode of Action (MoA) of novel drugs and to identify known and approved candidates for “drug repositioning”. MANTRA is a computational tool based on network theory and…

NFFinder
Web

NFFinder

A bioinformatics tool for identifying potential useful drugs in the context of…

A bioinformatics tool for identifying potential useful drugs in the context of orphan diseases. NFFinder uses transcriptomic data to find relationships between drugs, diseases and a phenotype of…

DPDR-CPI
Web
RANKS
Desktop

RANKS RAnking of Nodes with Kernelized Score functions

A flexible algorithmic scheme implemented and distributed as an R software…

A flexible algorithmic scheme implemented and distributed as an R software package. RANKS embeds kernelized score functions that have been successfully applied to gene function, gene disease…

MBiRW
Desktop

MBiRW

A novel computational method to identify potential novel indications for a…

A novel computational method to identify potential novel indications for a given drug. MBiRW utilizes some comprehensive similarity measures and Bi-Random walk algorithm. Drug similarity network and…

e-Drug3D
Dataset

e-Drug3D

A database of 3D chemical structures of drugs, providing several collections of…

A database of 3D chemical structures of drugs, providing several collections of ready-to-screen SD files of drugs fragments. The structure of each drug has been manually checked to assign the exact…

Drug voyager
Desktop

Drug voyager

Proposes a platform to construct a drug-specific pathway in which a…

Proposes a platform to construct a drug-specific pathway in which a molecular-level mechanism of action is formulated based on pharmacologic, pharmacogenomic, transcriptomic, and phenotypic data…

DMC
Web

DMC DrugMap Central

Enables the users to integrate, query, visualize, interrogate, and download…

Enables the users to integrate, query, visualize, interrogate, and download multi-level data of known drugs or compounds quickly for drug repositioning studies all within one system.

Cogena
Desktop

Cogena Co-expressed gene-set enrichment analysis

A fully configurable framework for co-expressed gene set enrichment analysis.…

A fully configurable framework for co-expressed gene set enrichment analysis. By combining pathway analysis and drug repositioning analysis, Cogena provides a unique approach to imply the drug mode…

Drug…
Dataset

Drug Repurposing Hub

Aims to discover new indications for existing drugs with known safety profiles.…

Aims to discover new indications for existing drugs with known safety profiles. Drug Repurposing Hub is an interactive website designed to rapidly identify drugs for evaluation in disease models. The…

DTIPRED
Desktop

DTIPRED

Enables the discovery of putative leads for drug repositioning that can be…

Enables the discovery of putative leads for drug repositioning that can be applied to any microbial proteome, as long as the interactome of interest is at least partially known. DTIPRED can be used…

A A A
DSigDB
Dataset

DSigDB Drug Signatures Database

A collection of drug and small molecule related gene sets based on quantitative…

A collection of drug and small molecule related gene sets based on quantitative inhibition and/or drug-induced gene expression changes data. DSigDB allows users to search, view, and download…

GIFT
Desktop
ksRepo
Desktop

ksRepo Kolmogorov-Smirnov Repo

A generalized tool for computational repositioning that builds on the successes…

A generalized tool for computational repositioning that builds on the successes of previous expression-based repositioning tools while allowing greater flexibility for the investigator. ksRepo…

PDOD
Web

PDOD Prediction of Drugs having Opposite effects on Disease genes

Identifies drugs having opposite effects on altered states of disease genes.…

Identifies drugs having opposite effects on altered states of disease genes. PDOD proposes a scoring function to discover drugs likely to restore altered states of disease genes using the path from a…

GoPredict
Web

GoPredict

A computational algorithm that allows patient stratification and drug…

A computational algorithm that allows patient stratification and drug repositioning. GoPredict uses comprehensive integration of genomics data, signaling pathway information, drug target databases…

PREDICT
Algorithm

PREDICT

An algorithm for the large-scale prediction of drug indications, that can…

An algorithm for the large-scale prediction of drug indications, that can handle both approved drugs and novel molecules. PREDICT is based on the observation that similar drugs are indicated for…

DRAR-CPI
Web

DRAR-CPI

A server for predicting drug repositioning and adverse reaction via…

A server for predicting drug repositioning and adverse reaction via chemical-protein interactome.

Integrity
Dataset

Integrity

Hosts a knowledgebase designed for drug discovery. The Integrity database…

Hosts a knowledgebase designed for drug discovery. The Integrity database contains a large collection of drugs which are annotated with information on their respective drug targets, the diseases they…

MeSHDD
Web
Desktop

MeSHDD MeSH-based Drug-Drug Similarity and Repositioning

A framework for computational drug repositioning using literature-derived…

A framework for computational drug repositioning using literature-derived drug-drug similarity. MeSHDD provides an alternate way of searching the biomedical corpus for novel (and existing) uses of…

Hetionet
Dataset

Hetionet

An integrative network encoding knowledge from millions of biomedical studies.…

An integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47031 nodes of 11 types and 2250197 relationships of 24 types. Data was integrated from 29…

Project…
Dataset

Project Rephetio Browser

Predicts new uses for existing compounds. Project Rephetio Browser uses machine…

Predicts new uses for existing compounds. Project Rephetio Browser uses machine learning to systematically learn network patterns of drug efficacy. This method translates the network paths between a…

RE:fine drugs
Dataset

RE:fine drugs

An interactive user interface to integrate GWAS and PheWAS reposition datasets…

An interactive user interface to integrate GWAS and PheWAS reposition datasets using Drug–Gene–Disease triads along with advanced search and export capabilities. ‘RE:fine drugs’ enables…

GeneExpressionS…
Desktop

GeneExpressionSignature

A package developed for the large-scale analysis of gene expression signatures.…

A package developed for the large-scale analysis of gene expression signatures. GeneExpressionSignature implements two rank-merging algorithms and two similarity-scoring algorithms. It provides a…

DPS
Desktop

DPS Drug Pair Seeker

A Java program that attempts to predict and prioritize pairs of drugs using the…

A Java program that attempts to predict and prioritize pairs of drugs using the Connectivity Map dataset. Users can enter lists of up and down differentially expressed genes from their own…

DRUGSURV
Dataset

DRUGSURV

A computational tool to estimate the potential effects of a drug using patient…

A computational tool to estimate the potential effects of a drug using patient survival information derived from clinical cancer expression data sets.

DR. PRODIS
Web

DR. PRODIS DRugome PROteome and DISeasome

A comprehensive proteome scale approach that predicts human protein targets and…

A comprehensive proteome scale approach that predicts human protein targets and side effects of drugs. We develop a comprehensive proteome scale approach that predicts human protein targets and side…

CRCMeta
Dataset

CRCMeta

A computational framework to integrate complex relationship among different…

A computational framework to integrate complex relationship among different types of data and infer the potential drug targets by using the semantic web technology, and to improve performance through…

DvD
Desktop

DvD Drug versus Disease

Provides a pipeline, available through R or Cytoscape, for the comparison of…

Provides a pipeline, available through R or Cytoscape, for the comparison of drug and disease gene expression profiles from public microarray repositories.

K-Map
Web

K-Map

A user-friendly web-based program that systematically connects a set of query…

A user-friendly web-based program that systematically connects a set of query kinases to kinase inhibitors based on quantitative profiles of the kinase inhibitor activities.

PharmDB
Dataset

PharmDB

A knowledge platform to rationally identify new indications for known FDA…

A knowledge platform to rationally identify new indications for known FDA approved drugs, which can be customized to specific projects using manual curation.

DMAP
Dataset

DMAP Drug directionality Map

An in silico drug-protein connectivity map, which contains directed…

An in silico drug-protein connectivity map, which contains directed drug-to-protein effects and effect scores. DMAP that can help drug development researchers evaluate what effects a drug may have on…

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