Targets, Target-ligand collections

 

  • 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
  • Pharos - The Target Central Resource Database (TCRD) which collates many heterogeneous gene/protein datasets and Pharos, a multimodal web interface that presents the data from TCRD (druggable genome) - database
  • PathAct - Actionable pathways - interactive discovery of therapeutic targets using signaling pathway models (suitability of potentially actionable genes, that could eventually become drug targets for personalized or individualized therapies) - online
  • DrugMiner - Comparative analysis of machine -learning algorithms for prediction of potential druggable proteins - database
  • Cancerin - Prediction of anticancer molecules using hybrid model developed on molecules screened against NCI -60 cancer cell lines. This server provides various facilities that includes; virtual screening of anticancer molecules, analog based drug design, and similarity with known anticancer molecules - online
  • NextProt - Exploring the universe of human proteins - database
  • READ DB - Database of RNA binding protein expression and disease dynamics - database
  • OnTheFly - OnTheFly database is a systematic determination of Drosophila melanogaster transcription factor DNA -binding specificities - database
  • EBI - The EBI Search engine - providing search and retrieval functionality for biological data from EMBL -EBI - database
  • PubAngioGen - A database and knowledge for angiogenesis and related diseases - database
  • MobiDB 2.0 - An improved database of intrinsically disordered and mobile proteins - database
  • BCL2DB - Database of BCL -2 family members and BH3 -only proteins - database
  • Coagulation proteins - Coagulation Factor Variant Databases supported by the European Association for Haemophilia and Allied Disorders (EAHAD) (2015) - database
  • Drug -drug - BEReX: Biomedical Entity -Relationship eXplorer. Allows users to find the shortest paths between two remote nodes, find the most relevant drugs, diseases, pathways and so on related to the current network, expand the network by particular types of entities and relations and modify the network by removing or adding selected nodes - standalone Java application
  • DGIdb - Mining the druggable genome. The tool provides an interface for searching lists of genes against a compendium of drug -gene interactions and potentially 'druggable' genes - online
  • ChEMBL -NTD - Neglected disease data - online
  • TIMETREE - It is a public resource for knowledge on the timescale and evolutionary history of life (eg, analysis of sequences) - online
  • Kinase SARfari - It is an integrated chemogenomics workbench focussed on Kinases. The system incorporates and Links Kinase sequence, structure, compounds and screening data - online
  • ADME SARfari - Predict likely ADME targets for an input molecule, Find ADME targets similar to an input FASTA sequence, Find ADME targets related to text terms, Find pharmacokinetic data relating to an input target, sequence or text term, Find activity/pharmacokinetic data for an input molecule or related compounds (via a similarity/substructure search), Match expression levels in human tissues for found targets - online
  • CREDO - CREDO is a relational database storing all pairwise atomic interactions of inter - as well as intra -molecular contacts between small - and macromolecules found in experimentally -determined structures from the Protein Data Bank (PDB) Structural variations from EnsEMBL Variation are mapped onto all protein structures in CREDO through the sequence -to -structure mapping. EnsEMBL Variation contains variation data from the most important sources, including dbSNP, COSMIC and UniProt as well as information about (disease) phenotypes that can be Linked to variations occurring in protein structures. This means that phenotypes can be Linked directly to ligand binding sites or protein -protein interfaces. Interactions between atoms are stored as Structural Interaction Fingerprints (SIFts) that were described first by Deng et al.. CREDO currently implements 13 different interaction types such as hydrogen bonds, halogen bonds, carbonyl interactions and others - database
  • MPSTRUC - Membrane proteins of known 3D structure - online
  • AlzPlatform - An Alzheimer's disease domain -specific chemogenomics knowledgebase for polypharmacology and target identification research - online
  • NRLiSt BDB - The NRLiSt BDB (Nuclear Receptors Ligands and Structures Benchmarking DataBase) is a non -commercial manually curated benchmarking database dedicated to the Nuclear Receptor(NR) ligands and structures pharmacological profiles - database
  • 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
  • MultitaskProtDB - A repository of multitasking proteins found in the literature. Multitasking or moonlighting is the capability of some proteins to execute two or more biological functions - online
  • EKPD - A hierarchical database of eukaryotic protein kinases (PKs) and protein phosphatases (PPs) - online
  • AgeFactDB - A database aimed at the collection and integration of ageing phenotype data including lifespan information. Ageing factors are considered to be genes, chemical compounds or other factors such as dietary restriction, whose action results in a changed lifespan or another ageing phenotype - online
  • SFLD - The Structure–Function Linkage Database is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies - online
  • TBDTBD - Tuberculosis Drug Target Database - online
  • PSICQUIC - PSICQUIC is an effort from the HUPO Proteomics Standard Initiative (HUPO -PSI) to standardise the access to molecular interaction databases programmatically - online
  • 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
  • ProtChemSI - A network of protein -chemical structural interactions (includes all existing 3D structures of complexes of proteins with low molecular weight ligands) - online
  • PTPs (Novo) - A Web -Accessible Resource of Information on Protein Tyrosine Phosphatases - online
  • TCDB - The Transporter Classification Database serves as a common reference point for transport protein research. The database contains more than 10 000 non -redundant proteins that represent all currently recognized families of transmembrane molecular transport systems - online
  • topPTM - Transmembrane (TM) proteins have crucial roles in various cellular processes. The location of post -translational modifications (PTMs) on TM proteins is associated with their functional roles in various cellular processes. Given the importance of PTMs in the functioning of TM proteins, this study developed topPTM (available online at ), a new dbPTM module that provides a public resource for identifying the functional PTM sites on TM proteins with structural topology - online
  • IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature is a collection of intrinsically disordered proteins (IDPs) that cannot adopt stable globular structures under physiological conditions - online
  • pE -DB - Open database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small -angle X -ray scattering and other data measured in solution - online
  • canSAR - A free, public cancer focused knowledgebase. It brings together biological, chemical, pharmacological and disease data, distills them and makes them accessible to cancer research scientists from all disciplines to support translational research and drug discovery - .
  • PPD - Plasma Proteome Database. This database contains information on 10 546 proteins detected in serum/plasma of which 3784 have been reported in two or more studies - online
  • Transformer (biotransformation of xenobiotics) - The simultaneous administration of several drugs can cause severe adverse effects based on interactions with the same metabolizing enzyme(s). The Transformer database contains integrated information on the three phases of biotransformation (modification, conjugation and excretion) of 3000 drugs and >350 relevant food ingredients (e.g. grapefruit juice) and herbs, which are catalyzed by 400 proteins. A total of 100 000 interactions were found through text mining and manual validation. The 3D structures of 200 relevant proteins are included - online
  • IUPHAR/BPS Guide to PHARMACOLOGY - 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 - online
  • SuperPain - A resource on pain -relieving compounds targeting ion channels. Database for pain -stimulating and pain -relieving compounds, which bind or potentially bind to ion channels that are involved in the transmission of pain signals to the central nervous system, such as TRPV1, TRPM8, TRPA1, TREK1, TRESK, hERG, ASIC, P2X and voltage -gated sodium channels. The database consists of about 8700 ligands, which are characterized by experimentally measured binding affinities. Additionally, 100 000 putative ligands are included - 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
  • Link - Genomics of Drug Sensitivity in Cancer - database
  • Bival -bind - Database of protein complexes with multivalent binding ability - Bival -bind - database
  • EuPathDB - Bioinformatics Resource Center for Biodefense and Emerging/Re -emerging Infectious Diseases is a portal for accessing genomic -scale datasets associated with the eukaryotic pathogens. One can find for instance ApiDB a unified entry point for the NIH -funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous databases. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of the genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as a database but as a single web -based point of entry that unifies access to three major existing individual organism databases (PlasmoDB.org, ToxoDB.org and CryptoDB.org), and integrates these databases with data available from additional sources... - database
  • MoDEL - MoDEL (Molecular Dynamics Extended Library) is a large library of molecular dynamics trajectories of representative protein structures - database
  • InterPro - It provides functional analysis of proteins by classifying them into families and predicting domains and important sites. It combines protein signatures from a number of member databases into a single searchable resource (see also InterProScan, a sequence analysis application) - online
  • KinBase - The kinase database - database
  • Kinweb - Collection of protein kinases encoded in the human genome - database
  • iHSP -PseRAAAC - iHSP -PseRAAAC - Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition - online
  • TransportDB - Genomic comparisons of membrane transport systems, membrane proteins - database
  • Dasty - Visualization and integration of protein sequence feature annotations via DAS (All biological information about a protein) - .
  • CARGO - A web portal to integrate customized biological information (at present CARGO displays biological information only for human genes). Cargo takes information from 41 databases, and SNP3D, iHop, OMIN, FunCUT, Enviro (protein interactions)... - .
  • SugarBindDB - Lists pathogen and biotoxin lectins and their carbohydrate ligands in a searchable format - database
  • 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
  • CTD2 - Cancer Target Discovery and Development - USA cancer project
  • TiPs - A database of therapeutic targets in pathogens and associated tools - database
  • HIT - Linking herbal active ingredients to targets - online
  • ChromoHub - A data hub for navigators of chromatin -mediated signalling - online
  • PLI - A web -based tool for the comparison of protein -ligand interactions observed on PDB structures - database
  • GRAC - Guide to Receptors and Channels provides a succinct overview of the key properties of over 1600 established or potential pharmacological targets - database
  • HORDE -  The Human Olfactory Data Explorer is a database of human Olfactory Receptors (ORs), ORs are G -Coupled Protein Receptors - database
  • TCBD - Transporter Classification (TC) system - database
  • MEROPS - An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them - database
  • Link - the Common Molecules collection, part of the Reciprocal Net project. The molecules in this site are considered common based on their general use or presence in the world in and around us or by the interest they spark because of their fascinating structural properties and innovative applications - database
  • ASD - the AlloSteric Database, the first online database which provides a central resource for the display, search and analysis of the structure, function and related annotation for allosteric molecules - database
  • UniProt - The mission of UniProt is to provide the scientific community with a comprehensive, high -quality and freely accessible resource of protein sequence and functional information - database
  • MATADOR -  A resource for protein -chemical interactions. It differs from other resources such as DrugBank in its inclusion of as many direct and indirect interactions as we could find. In contrast, DrugBank usually contains only the main mode of interacton. The manually annotated list of direct (binding) and indirect interactions between proteins and chemicals was assembled by automated text -mining followed by manual curation - database
  • canEvolve - A Web Portal for Integrative Oncogenomics - online
  • BioModels -  Database - repository of computational models in biology - online database
  • PDBe - The EBI has a developed and maintained a number of protein structure related databases. The Protein Databank in Europe (PDBe) group, within the EBI, is responsible for the deposition and validation of new protein structures - online database
  • Brenda - The Comprehensive Enzyme Information System - online database
  • Enzyme Portal - A case study in applying user -centred design methods in bioinformatics - database
  • PSMDB -  The protein -small -molecule database, a non -redundant structural resource for the analysis of protein -ligand binding - database online
  • EC -PDB -  Contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB) - online database
  • HMRbase -  Manually curated database of Hormones and their Receptors - online database
  • SDAP -  Web server that integrates a database of allergenic proteins with various computational tools that can assist structural biology studies related to allergens - online
  • KChannelDB - A Molecular Specific Information System for Potassium channels - online database
  • NucleaRDB -  An Information System for Nuclear Receptors - online database
  • Genome3D - A UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains - Annotating Genomes with Structures, many tools
  • NPIDB - Nucleic acid protein interaction database - database online
  • Glycan - Glycan fragment database - a database of PDB -based glycan 3D structures - online database
  • KIDFamMap - A database of kinase -inhibitor -disease family maps for kinase inhibitor selectivity and binding mechanisms - online database
  • SeRAPhiC - Dataset of about 50 high -quality protein -fragment complexes - datasets
  • BAPPL -  About 161 protein -ligand complexes with experimental and estimated binding free energies - datasets
  • AtlasCBS -  A tool that allows you to explore chemico -biological space using Ligand Efficiency Indices (LEIs) as variables - navigate in Chemico -Biological Space
  • CSAR -  A Resource for Docking and Scoring Development Community Structure -Activity Resource - .
  • MIPS -  Mammalian Protein -Protein Interaction Database - online
  • Negatome - A collection of protein and domain pairs which are unlikely engaged in direct physical interactions - Macromolecules, database
  • GPCRDB - GPCRDB - GPCR -specific PDF reader - .
  • GPCR SARfari -  Integrated chemogenomics workbench focussed on GPCRs - GPCR Database
  • GDD - GPCR Decoy Database, with its accompanying GPCR Ligand Library (GLL) have been compiled to help in GPCR docking. C Cavasotto - GPCR -ligand Database
  • kinase.com -  Explores the functions, evolution and diversity of protein kinases, the key controllers of cell behavior - database
  • GLIDA - GPCR ligand database - GPCR -ligand Database
  • SuperTarget -  Integrates drug -related information, over 6000 targets, 195000 compounds, 282 drug -target pathways...57 CYP - Compound Database, Macromolecules
  • PDSP - The database has 46,134 Ki values for searching... (PDSP Ki Database)
    - database
  • Iridium - A Highly Trustworthy Protein -Ligand Structure Database - database, dataset
  • AutoBind -  Automatic extraction of protein -ligand -binding affinity data - online
  • PDBbind - Macromolecules with co -crystallized ligands and experimental binding affinities - Compound Database, Macromolecules
  • Scorpio -  Structure -calorimetry of reported protein interactions online - This is a FREE online repository of protein -ligand complexes which have been structurally resolved and thermodynamically characterized - database
  • RELIBASE - Proteins with co -crystallized ligands and CavBase - compound database, macromolecules
  • BioLiP -  Biologically relevant ligand -protein binding interactions is a semi -manually curated database for high -quality - database
  • DTome - Drug -Target Interactome - compound database, macromolecules
  • Astex set - CCDC/Astex validation test set - 305 protein -ligand complexes to calibrate docking and scoring tools - datasets
  • AffinDB - Proteins with co -crystallized ligands and experimental binding affinities - database
  • LIBP -Pred - Web server for lipid binding proteins - online
  • VeryGene - Linking tissue -specific genes to diseases, drugs, and beyond for knowledge discovery - database
  • Trypano -PPI - Prediction of unique targets in trypanosome proteome - online
  • SuperPred - Drug classification and target prediction - online
  • PDTD - A web -accessible protein database for drug target identification - online
  • KEGG - Kyoto Encyclopedia of Genes and Genomes - online database
  • Cmap - The Connectivity Map is a collection of genome -wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern -matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene -expression changes - online database
  • sscMap - Connecting small -molecule drugs using gene -expression signatures - standalone
  • DvD -  R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data - standalone
  • DIGEP -Pred - In silico prediction of drug -induced gene expression profiles based on structural formula - online
  • PRIDE - The PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post -translational modifications and supporting spectral evidence - database
  • GeneBank - DNA sequences - database
  • Omnibus - Gene Expression Omnibus - a public functional genomics data repository - database
  • TDD -  Therapeutic Target Database - online database
  • DTome - Drug -Target Interactome - compound Database, Macromolecules
  • SuperTarget - SuperTarget integrates drug -related information - compound Database, Macromolecules
  • TissueDistributionDBs - A repository of tissue distribution profiles for identifying and ranking the genes in the spectrum of tissue specificity based on Expressed Sequence Tags (ESTs)  - online
  • ADMET targets - DART (Ji et al. 2003), ADME -AP (Sun et al. 2002), TRMP (Zheng et al. 2004), TTD (Chen et al. 2002a) - databases for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion associated proteins. Therapeutic Target Database (268 successful targets in TTD in May 2007)   - databases for ADME/tox, Toxicity
  • HEMD - An integrated tool of human epigenetic enzymes and chemical modulators for therapeutics - database
  • Last updated on .

Email

bruno.villoutreix(at)gmail.com

Address

Follow me


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