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URLs

Off-targets

polypharmacology

Adverse drug reactions (ADR)

prediction of bioactivity

repositioning

repurposing

Comments
LigDig Which proteins does my ligand inhibit in a network and why online
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