Useful links

Databases of drugs and drug targets

  • BindingDB: The Binding Database
  • ChEMBL: medicinal chemistry and drug discovery databases
  • DrugBank: detailed information on drugs and the protein sequences they interact with. Note that DrugBank is free for academic and non-profit use but commercial users require a license.
  • GLIDA: GPCR-Ligand Database
  • NIMH-PDSP Ki Database
  • PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base
  • PubChem: a free database of chemical structures of small organic molecules and information on their biological activities
  • TTD: Therapeutic Target Database
  • ZINC: A database containing commercially available compounds for structure-based virtual screening.

GPCR databases

  • GDR 3545: group of researchers in France on "G protein-coupled receptors - from physiology to drugs"
  • Endogenous GPCR List
  • GPCRDB: Information system for G protein-coupled receptors (GPCRs)
  • gpDB: a database of G-proteins and their interaction with GPCRs
  • HORDE: The Human Olfactory Data Explorer
  • ORDB: Olfactory Receptor DataBase
  • GPCR-OKB: The G Protein Coupled Receptor Oligomerization Knowledge Base Project
  • Structure modeling of 907 G protein-coupled receptors in the human genome (Zhang Y, Devries ME, Skolnick J. PLoS Comput Biol. 2006 2(2):e13)

VGIC and LGIC databases

  • LGICdb: Ligand Gated Ion Channel Database
  • VKCDB: Voltage-gated Potassium Channel Database

Nuclear Receptor databases

  • NURSA: Nuclear Receptor Signaling Atlas

Enzyme databases

  • EBI Enzyme Portal
  • ExplorEnz: A resource providing access to the data of the International Union of Biochemistry and Molecular Biology (IUBMB) Enzyme Nomenclature List, and which maintains the IUPAC standard formatting of chemical names.
  • PhosphoSitePlus: An expert curated database providing access to information and tools useful to the study of in-vivo post-translational modification of proteins of the kinome.

Transporter databases

  • SLC Tables: information on Solute Carrier transporter families
  • Transporter Classification Database

Antibody resources

  • IMGT®, the international ImMunoGeneTics information system®, which hosts IMGT/mAb-DB, a database of monoclonal antibodies (IG, mAb) and fusion proteins for immune applications (FPIA)
  • Marketed therapeutic antibodies compendium

Gene/protein databases

  • GeneCards: A searchable, integrated, database that provides concise genomic related information, on all known and predicted human genes. Includes MalaCards, the human disease database. Note that GeneCards is free for academic and non-profit use but commercial users require a license.
  • InterPro: integrates protein information from several allied databases into a single searchable resource providing protein family classification information, functional domain prediction and identification of other important sites on proteins.
  • HomoloGene: An automated system for constructing putative homology groups from the genomes of a wide range of eukaryotic species.
  • HUGO Gene Nomenclature Committee (HGNC)
  • KEGG: Kyoto Encyclopedia of Genes and Genomes
  • neXtProt: a human protein-centric knowledgebase providing access to a range of high-quality datasets with tools to mine them.
  • Pfam: a collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
  • Protein Ontology: an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them.
  • Treefam: a database of animal gene trees, encompassing inferred phylogenetic trees, predicted orthologues/parologues and the evolutionary history of genes.
  • UniGene: a database of the transcriptome providing information on protein similarities, gene expression, cDNA clones, and genomic location.
  • UniProt: resource for protein sequence and functional information

Metabolite databases

  • HMDB: Human Metabolome Database
  • LIPID MAPS: Nature Lipidomics Gateway

Other relevant resources

  • CCL: Computational Chemistry List
  • 7TMRmine: a Web server for mining of 7TM proteins

Journals

  • British Journal of Clinical Pharmacology
  • British Journal of Pharmacology
  • Drug Discovery Today
  • European Journal of Pharmacology
  • Hospital Pharmacology
  • Journal of Cheminformatics
  • The Journal of Pharmacology and Experimental Therapeutics
  • Molecular Pharmacology
  • Nature Reviews Drug Discovery
  • Pharmacological Reviews
  • Pharmacology Research & Perspectives

Other useful links

  • IUPHAR Career Centre - PharmacoCareers.org

UoE Teaching Materials (Jan 2019)

  • Database Interrogation Exercise (Dr. Adam Pawson)
http://pillsbank.net