The BindingDB is a public database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds.The database currently contains data generated by isothermal titration calorimetry, enzyme inhibition, and receptor-ligand binding methods.
The BMCD stores information on protein and nucleic acid crystals that have been reported in the literature or deposited in the Protein Data Bank. Crystal growth conditions have been parsed into separate chemicals with numerical concentrations to faciliate data mining. The mission of the BMCD is to enable the discovery of relations among protein properties, crystal conditions, and crystal behavior, in order to facilitate the design of crystal screening strategies for the determination of new structures.
Free database containing information on over 6500 enzymes: nomenclature, EC and registry numbers, reaction and specificity, inhibitors, structure, isolation, literature references, etc. (Technical University of Braunschweig)
Provides "results of 6540 chronic, long-term animal cancer tests on 1547 chemicals. The CPDB provides easy access to the bioassay literature, with qualitative and quantitative analyses of both positive and negative experiments that have been published over the past 50 years in the general literature through 2001 and by the National Cancer Institute/National Toxicology Program through 2004." Note: not updated since 2011.
"ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).
The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs." (European Bioinformatics Institute)
"Bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information." The database contains >13,000 drug entries including 2600 FDA-approved small molecule drugs, 1300 FDA-approved biotech (protein/peptide) drugs, 130 nutraceuticals and over 6300 experimental drugs. Additionally, 5200 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.
"ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided." (ExPASy)
Search by name, application, specificity or EC number. The Enzyme Explorer also features detailed sites on metabolic pathways, protein kinases, protease specificity and inhibition, and glycoprotein analysis as well as new cell signaling, analytical and diagnostic enzymes and reagents. (Sigma-Aldrich)
Subtitle: "Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse." Browse and search for enzyme names using EC numbers.
"ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc."
"GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI."
"The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data."
"LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major and many minor lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation." (NIH)
Free web site with Java-based (JME) interface for searching substructure, similarity and pharmacophore similarity on a collection of molecules. Also offers a chemical property calculation function for determining estimated logP (octanol-water partition coefficient), PSA, etc.
Open access database designed to cover all microbially-derived natural products published in the peer-reviewed primary scientific literature. This encompasses bacterial, fungal and cyanobacterial compounds, but does not include compounds from plants, invertebrates or other higher organisms unless these compounds have also been explicitly identified from a microbial source. Compounds from lichens and mushrooms and other higher fungi are included. Compounds from marine macro algae and diatoms are excluded. (Simon Fraser Univ.)
"The NDB contains information about experimentally-determined nucleic acids and complex assemblies.
Use the NDB to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and learn about nucleic acids." (Rutgers University)
A wiki site that aims to collect, organize and disseminate structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules.
Open cheminformatics database on properties and biological activities of small molecules, primarily of interest to pharmaceutical and chemical genomics researchers, plus larger molecules such as nucleotides, carbohydrates, lipids, peptides, and chemically-modified macromolecules. Records are contributed by many sources, including government agencies, publishers, vendors, and individual researchers. (NIH/NLM)
"A curated database containing structured information about biochemical reactions and their corresponding kinetics. It describes participants and modifiers of the reactions, as well as measured kinetic data (including kinetic rate equations) embedded in their experimental and environmental context."
"Structural Classification of Proteins” extended (SCOPe) is a database of protein structural relationships that extends the SCOP database. SCOP is a (mostly) manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships." (UC Berkeley)
STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. STITCH contains interactions between 500,000 small molecules and 9.6 million proteins from over 2000 organisms.