Off-targets, repurposing, repositioning hypotheses

 

  • LigDig - Which proteins does my ligand inhibit in a network and why - online
  • PPB - Polypharmacology Browser searches through 4613 groups of at least 10 bioactive molecules with documented activity against a biological target listed in ChEMBL. To identify analogs, the query molecule is investigated using several different fingerprints - online
  • DRH - Drug Repurposing Hub - online
  • repoDB - Database to test drug repositionings - database
  • RepurposeDB - Small Molecule and Protein-Drug Similarity Search. RepurposeDB (Explore repositioned drug) - database
  • DRABAL - Novel method to mine large high-throughput screening assays using Bayesian active learning - standalone
  • DPDR-CPI - A server that predicts Drug Positioning and Drug Repositioning via Chemical-Protein Interactome - online
  • Gusar - Gusar antitargets - online
  • CoFFer - Off targets - online
  • iATC-mISF - A multi-label classifier for predicting the classes of anatomical therapeutic chemicals (ATC) - online
  • DT-Web - A web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference - online
  • CMC - A Server for Combinatorial Drug Toxicity and Efficacy Analysis - online
  • DrugCentral - Online drug compendium (2016) - online (database)
  • DASPfind - New Efficient Method to Predict Drug-Target Interactions - online
  • PLIC - Protein-ligand interaction clusters - online
  • CS-MINER - A Tool for Association Mining in Binding-Database (compare the relative position of active biosimilar molecules in chemical space) - online
  • openFDA - Open-source APIs and a developer community for FDA data - online
  • MBiRW - It utilizes some comprehensive similarity measures and Bi-Random walk (BiRW) algorithm to identify potential novel indications for a given drug - standalone
  • Pharmacophore - Pharmacophore-Map-Pick: A Method to Generate Pharmacophore Models for All Human GPCRs. A total of 2386 pharmacophore models for 819 different GPCRs (99 % coverage (819/825) - online
  • PhIN - Protein pharmacology interaction network database (PhIN) aiming to assist multitarget drug discovery - online
  • DrugQuest - DrugQuest is a text mining tool for knowledge discovery: it is designed to cluster DrugBank records based on text attributes in order to find new associations between drugs - online
  • NIH Clinical - NIH Clinical Collection - online
  • NCGC - Pharmaceutical Collection: A comprehensive resource of clinically approved drugs enabling repurposing and chemical genomics - online
  • EMA - European Medicines agency - online
  • ACTP - A webserver for predicting potential targets and relevant pathways of autophagy-modulating compounds - online
  • DNetDB - The human disease network database based on dysfunctional regulation mechanism - online
  • IDAAPM - Integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data - online
  • C2MAP DMAP - C2MAP (C2Maps): Disease specific drug to gene association (A network pharmacology database with comprehensive disease-gene-drug connectivity relationships). DMAP: Chemicals (include drugs) to protein directly interaction (drug-drug-similarity-based method, drug repositioning prediction can be done using DMAP) - online (URL Link unclear)
  • systemsDock - A web server for network pharmacology-based prediction and analysis - online
  • ChemProt 3.0 - A global chemical biology diseases mapping - database
  • DSEA - Drug-Set Enrichment Analysis—DSEA based on drug-induced gene expression profiles, is able to identify the molecular pathways that are targeted by most of the drugs in the set. By diluting drug-specific effects unrelated to the phenotype of interest, DSEA is able to highlight phenotype-specific pathways, thus helping to formulate hypotheses on the MoA (mechanism of action) shared by the drugs in the set - online
  • PDID - A database of molecular-level putative protein-drug interactions in the structural human proteome - online
  • CMapBatch - Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data (Repurposing) - standalone
  • iDTP - A novel integrated structure- and system-based approach of drug-target prediction (iDTP) to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and metabolites (collectively called ‘drugs’) (probabilistic pocket ensemble (PPE)) - standalone
  • Bio-AIMS - Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models. Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins (2015) - online
  • SPiDER - Identifying the macromolecular targets of de novo designed chemical entities through self-organizing map consensus. SPiDER Target Prediction Software - online
  • DSigDB - Drug Signatures Database for Gene Set Analysis - online & database
  • FNTM - A server for predicting functional networks of tissues in mouse - online
  • drugable.com - Could help for repositioning - online
  • CSNAP - Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens - online
  • Galahad - A web server for drug effect analysis from gene expression - online
  • CBC lab - Drug repositioning by integrating target information through a heterogeneous network model - online
  • SPACE - Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources - database
  • IntoGen - Integrative Onco Genomics (cancer, mutations, drug repositioning) - online & database
  • MACE - Mutation-oriented profiling of chemical response and gene expression in cancers - database
  • MTLD - Database of Multiple Target Ligand, which was built through data mining of the Protein Data Bank. The MTLD contains 1,732 multiple-target ligands (MTLs) which bind to 14,996 binding sites extracted from 12,759 PDB structures. Among MTLs, 222 entries are approved drugs and 1,334 entries are drug-like compounds - database
  • ASDCD - Antifungal synergistic drug combination database - database
  • GraphSAW - A web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data (partially commercial) - online
  • Patch - The server (Patch-Surfer2.0) predicts binding ligands for a protein pocket (2014) - online
  • TarPred - TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds. Given a query compound structure, it provides the top ranked 30 interacting targets. For each of them, TarPred not only shows the structures of three most similar ligands that are known to interact with the target, but also highlights the disease indications associated with the target - online
  • PRODIS - Comprehensive prediction of drug-protein interactions, side effects for the human proteome. This server will screen your molecule against pre-computed target library. Top targets with mTC >= 0.9 (or top 350 ) will be returned. You can also search the pre-computed DR. PRODIS database for DrugBank drugs against the human proteome. Human protein target structure models and ligand binding sites are also available - online
  • AERS - AERS spider: An online interactive tool to mine statistical associations in Adverse Event Reporting System Pharmacoepidemiology and Drug Safety (2014) - online
  • LINCS - LINCS Canvas Interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures - Online
  • LINCS - LINCS aims to create a network-based understanding of biology by cataloging changes in gene expression and other cellular processes that occur when cells are exposed to a variety of perturbing agents, and by using computational tools to integrate this diverse information into a comprehensive view of normal and disease states that can be applied for the development of new biomarkers and therapeutics. By generating and making public data that indicates how cells respond to various genetic and environmental stressors, the LINCS project will help gain a more detailed understanding of cell pathways and aid efforts to develop therapies that might restore perturbed pathways and networks to their normal states - .
  • SuperPred - Drug classification and target prediction. The drug classification for a compound can be performed at the Drug Classification site. Target prediction for an input compound can be executed at the Target-Prediction site. The Anatomical Therapeutic Chemical (ATC) classification system is used for the classification of drugs. It is published by the World Health Organization (WHO). The classification is based on therapeutic and chemical characteristics of the drugs. - online
  • IntSide - A web server for the chemical and biological examination of drug side effects - online
  • DINIES - DINIES (drug-target interaction network inference engine based on supervised analysis) is a web server for predicting unknown drug-target interaction networks from various types of biological data (e.g. chemical structures, drug side effects, amino acid sequences and protein domains) in the framework of supervised network inference - online
  • LigSearch - A knowledge-based web server to identify likely ligands for a protein target (aimed at predicting ligands that might bind to and stabilize a given protein) - online
  • LTMap - A web server for assessing the potential liver toxicity by genome-wide transcriptional expression data. In LTMap, researchers could compare signatures of query compounds against a pregenerated signature database of 20 123 Affymetrix arrays associated with about 170 compounds retrieved from the largest public toxicogenomics data set Open TG-GATEs - online
  • CDRUG - A Web Server for predicting anticancer efficacy of chemical compounds. It is based on NCI60 database and is powerful for large scale prediction - online
  • Link - eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models - Online
  • iRAISE - Facing the Challenges of Structure-based Target Prediction by Inverse Virtual Screening - .
  • GUILDify - A web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms  - Online
  • Balestra - BalestraWeb: Efficient, online evaluation of drug-target interactions - Online
  • iDrug - A web-accessible and interactive drug discovery and design platform. Computer-aided drug design based on pharmacophore and 3D molecular similarity searching. The web interface enables binding sites detection, virtual screening hits identification, and drug targets prediction in an interactive manner through a seamless interface to all adapted packages (e.g., Cavity, PocketV.2, PharmMapper, SHAFTS). Several commercially available compound databases for hit identification and a well-annotated pharmacophore database for drug targets prediction were integrated in iDrug as well. The web interface provides tools for real-time molecular building, editing, converting, displaying, and analyzing - online
  • Disease - DiseaseConnect: a comprehensive web server for mechanism-based disease–disease connections - online
  • DINIES - Drug–target interaction network inference engine based on supervised analysis - online
  • Link - AlzPlatform: An Alzheimer's disease domain-specific chemogenomics knowledgebase for polypharmacology and target identification research - online
  • ProBiS - Probis-ligands: A web server for prediction of ligands by examination of protein binding sites - online
  • MCSS - A multi-fingerprint browser for the ZINC database. To confirm the activity of an initial small molecule hit compound from an activity screening, one needs to probe the structure–activity relationships by testing close analogs. The multi-fingerprint browser assists this process - online
  • Alkemio - Association of chemicals with biomedical topics by text and data mining - online
  • Link - DRUGSURV: a resource for repositioning of approved and experimental drugs in oncology based on patient survival information. It covers both approved drugs (about 1700) as well as experimental drugs (about 5000) - online
  • Link - chemical-protein interactions (CPI) spectrum - online
  • ChemBio - ChemBioNavigator: Navigate at the interface of chemical and biological data. Based on the OpenPHACTS platform for drug discovery - online
  • SMAP - SMAP software package is designed for the comparison and the similarity search of protein three-dimensional motifs independent on the sequence order - online
  • DTome - DTome: a web-based tool for drug-target interactome construction - online
  • Link - CPI-Predictor: Molecular polypharmacology, off-targets and drug repositioning focused on G protein-coupled receptors and kinome - online
  • Link - SwissTargetPrediction: This website allows users to predict the targets of a small molecule. Using a combination of 2D and 3D similarity measures, it compares the query molecule to a library of 280000 compounds, active on more than 2000 targets of 5 different organisms - online
  • PSICQUIC - PSICQUIC is an effort from the HUPO Proteomics Standard Initiative (HUPO-PSI) to standardise the access to molecular interaction databases programmatically - online
  • PathDB - ConsensusPathDB: Integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways. Data originate from currently 32 public resources for interactions (listed below) and interactions that we have curated from the literature. The interaction data are integrated in a complementary manner (avoiding redundancies), resulting in a seamless interaction network containing different types of interactions - online
  • Link - ProtChemSI: A network of protein-chemical structural interactions (includes all existing 3D structures of complexes of proteins with low molecular weight ligands) - online
  • FTC - The Functional Therapeutic Chemical Classification System defines over 20'000 mechanisms and modes of action for approved drugs - online
  • IUPHAR - The International Union of Basic and Clinical Pharmacology British Pharmacological Society (IUPHAR/BPS) Guide to PHARMACOLOGY is an expert-driven knowledgebase of drug targets and their ligands (also named GtoPdb, guide to pharmacology database)
    - online
  • CTD-Pfizer - CTD illuminates how environmental chemicals affect human health. Manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions - online
  • DIGEP-Pred - Web service for in silico prediction of drug-induced gene expression profiles based on structural formula (drug repositioning...) - online
  • PTID - An integrated web resource and computational tool for agrochemical discovery (Pesticide-Target interaction database (PTID), which comprises a total of 1347 pesticides with rich annotation of ecotoxicological and toxicological data as well as 13 738 interactions of pesticide-target and 4245 protein terms via text mining) through the integration of ChemMapper, an in-house computational approach to polypharmacology, PTID can be used as a computational platform to identify pesticides targets and design novel agrochemical products - online
  • DMC - DrugMap Central: an on-line query and visualization tool to facilitate drug repositioning studies - online NIH project
  • NCATS - Rescuing and Repurposing Drugs - online NIH project
  • HitPick - A web server for hit identification and target prediction of chemical screenings - online
  • DT-Hybrid - Drug-target interaction (DTI) prediction through domain-tuned network-based inference. DT-Hybrid is an R package that implements the homonymous algorithm for the prediction of interactions between small-molecules (i.e. Drug-Target Interactions) - standalone
  • Link - ChemMapper: A versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method - online
  • EU-ADR - Web Platform Exploring and Understanding Adverse Drug Reactions By Integrative Mining of Clinical Records and Biomedical Knowledge - online, need to register
  • Offsides - Offsides and Twosides: Data-Driven Prediction of Drug Effects and Interactions: database of drug effects (Offsides) and a database of drug-drug interaction side effects (Twosides) (Altman lab)  should be also available at PharmGKB - datasets
  • PharmGKB -  Knowledge base that captures the relationships between drugs, diseases phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD) - ADME/tox; PK/PD
  • Natural - Natural-Product-Likeness: This scoring system is implemented as Taverna 2.2 workflows. The present Link goes to the executable standalone java package (under Academic Free License) - standalone
  • Link -  FINDSITE-COMB: see also FINDSITE-LHM, a homology modeling approach to flexible ligand docking, and Curr Opin Struct Biol. 2013 Feb 14, by Skolnick J et al - online
  • Link - Molinspiration: Predict bioactivity, Score a compound for its ability to be GPCR ligand, ion channel modulator, kinase inhibitor, nuclear receptor ligand, protease inhibitor, enzyme inhibitor. Based on Bayesian statistics to compare structures of representative ligands active on the particular target with structures of inactive molecules and to identify substructure features (which in turn determine physicochemical properties) typical for active molecules - online
  • FAERS - The FDA Adverse Event Reporting System is a database that contains information on adverse event and medication error reports submitted to FDA - database
  • DIDB - The Metabolism and Transport Drug Interaction Database and the Pharmacogenetics Database (e-PKGene) are part of a knowledge base (DIDB platform) designed for scientists and clinicians working in the field of drug development, drug disposition and drug-drug interactions (DDIs). The DIDB platform was developed at the University of Washington s Department of Pharmaceutics, School of Pharmacy with input from pre-clinical and clinical pharmaceutical scientists. The DIDB was first licensed in 2002 and is currently used by a large number of pharmaceutical companies, regulatory agencies, contract research organizations and academic institutions worldwide - database commercial
  • CYP - P450 Drug Interaction Table - database
  • CPRD - The Clinical Practice Research DataLink is the new English NHS observational data and interventional research service, jointly funded by the NHS National Institute for Health Research (NIHR) and the Medicines and Healthcare products Regulatory Agency (MHRA). CPRD services are designed to maximise the way anonymised NHS clinical data can be Linked to enable many types of observational research and deliver research outputs that are beneficial to improving and safeguarding public health - database
  • SuperToxic - SuperToxic database - database
  • VAERS - The Vaccine Adverse Event Reporting System - database
  • VigiBase -  Unique collection of international drug safety data. The data is available in a wide range of services, from advanced statistical analysis to basic case report retrieval - database, commercial
  • PharmaTrek - Polypharmacology - online
  • ChemBl - ChemBl - online
  • Link - Chem2Bio2RDF: A semantic framework for Linking and data mining chemogenomic and systems chemical biology data - Polypharmacology, ADR, off-targets, online
  • Link - FragmentStore: A comprehensive database of fragments Linking metabolites, toxic molecules and drugs - database - database
  • SePreSA -  A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calculated using DOCK program - Small molecule docking - admet - off-targets, online
  • Link - BioDrugScreen: Computational drug design and discovery resource and server. The portal contains the DOPIN (Docked Proteome Interaction Network) database constituted by millions of pre-docked and pre-scored complexes from thousands of targets from the human proteome and thousands of drug-like small molecules from the NCI diversity set and other sources. The portal is also a server that can be used to (i) customize scoring functions and apply them to rank molecules and targets in DOPIN; (ii) dock against pre-processed targets of the PDB; and (iii) search for off-targets - online
  • Link - The ElectroShape Polypharmacology server is a tool that enables any user to estimate polypharmacology profiles and side effects of compounds based on the molecular similarity concept - off-target, online
  • Link -  TargetHunter: Designed and constructed to identify possible targets of small molecules by searching the available bioactive compound-target pairs from various resource using the query structure - off-target, online
  • ChemProt2 - A disease chemical biology database. Profiling - disease chemical biology database off-target, online
  • PASS Inet -  Predicts over 4000 kinds of biological activity, including pharmacological effects, mechanisms of action, toxic and adverse effects, interaction with metabolic enzymes and transporters, influence on gene expression, etc. - off-target, tox...online
  • AMBIT - The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) Links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface - standalone
  • GUSAR - Quantitative prediction of antitarget interaction profiles for chemical compounds - online
  • STITCH - Chemical-Protein Interactions - Chemical-Protein Interactions -  off-target, online
  • TarFisDock -  A web server for identifying drug targets with docking approach - off-target, online
  • DRAR-CPI - Drug repositioning and adverse drug reaction - repositioning and Tox, online
  • PubChem - PCPromiscuity (pubchem promiscuity): A web resource for gathering compound promiscuity data from PubChem - drug-repositioning off-target, online
  • Link - PROMISCUOUS: A database for network-based drug-repositioning - drug-repositioning off-target
  • Link -  PharmMapper: Designed to identify potential target candidates for the given probe small molecules - off-target, online
  • SEA -             Similarity ensemble approach - off-target, online
  • SuperDrug -  Contains  about 2.396 compounds - Drug Database
  • PDSP - NIMH Psychoactive Drug Screening Program - CNS
  • DrugBank - Numerous data about drugs and targets including drugs already in use (metabolism....) - Drug Database
  • Drug3k - Prescription drug information for consumers - Prescription drug information for consumers
  • SIDER - SIDER 2 - online
  • idTarget - A server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach - online
  • e-Drug3D -  Offers a facility to explore FDA approved drugs - online
  • Last updated on .

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© Bruno Villoutreix. A first version of this Website was launched in 2006. Thank to Natacha Oliveira