Biochemistry

AlphaFold DB provides open access to protein structure predictions for the human proteome and 20 other key organisms.

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.

BioCyc is a collection of 17831 Pathway/Genome Databases (PGDBs) for model eukaryotes and for thousands of microbes, plus software tools for exploring them. BioCyc is an encyclopedic reference that contains curated data from 130,000 publications. Subscription is required for unlimited use. (SRI International)

An online training course for learning about this expanding field. (EMBL-EBI UK)

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.

BMRB collects, annotates, archives, and disseminates spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. (Univ. of Connecticut)

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)

Dictionary of small molecular entities that are natural or synthetic products used to intervene in the processes of living organisms. Data drawn from public files such as IntEnz and KEGG LIGAND, etc. (EMBL-EBI)

ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. (European Bioinformatics Institute)

ChemDB is a suite of chemical datasets and learning tools created by UC Irvine. Includes a chemical search feature for about 4 million compounds from vendor catalogs.

Tool to find and use evaluated small-molecule reagents called chemical probes in biomedical research and drug discovery. Chemical probes are potent, cell-active, well-characterised small-molecule modulators of protein function. They are mostly inhibitors, but can also be activators, (ant)agonists or degraders or other kinds of modulators, which can be used to perturb a target protein in biological systems.

CTD provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are integrated with functional and pathway data to aid in development of hypotheses about the mechanisms underlying environmentally influenced diseases.

DrugBank Online is a free online database containing information on drugs and drug targets. It combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

Provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic action for >4700 drugs. Monitors FDA, EMA, and PMDA for new drug approvals. (UNM Medical School)

EMBL-EBI web services allow you to query large biological data resources programmatically. The Web Services technology are built on open standards.

"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)

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 bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools, developed by SIB Groups and supporting a range of life science and clinical research domains, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry."

"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."

Contains the reference sequence and working draft assemblies for a large collection of genomes. (UC Santa Cruz)

"GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences." (Kyoto University)

"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." (The Metabolomics Innovation Centre, Canada)

Contains reusable images.

NIH protein crystallography repository.

LIPID MAPS Lipidomics Gateway provides access to lipid nomenclature, databases, tools, protocols, standards, tutorials, meetings, publications, and other resources. (UK)

Open source mass spectral library for the identification of small chemical molecules of metabolomics, exposomics and environmental relevance. The vast majority of MassBank contents now features high-resolution mass spectrometry data, although all kinds of mass spectral data are accepted.

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.

Parent site of the major NLM databases, including PubMed, GenBank, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, PubChem, and others. (NIH)

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.)

NAKB provides search, report, statistics, atlas and visualization pages for all nucleic-acid containing experimentally determined 3D structures held by NDB and by the Protein Data Bank (PDB), including all major methods: X-ray, NMR, and Electron Microscopy. For each structure, links are provided to external resources that annotate and analyze nucleic acid structures and their complexes. (Rutgers Univ.)

Calculates on-the-fly drug-relevant properties (cLogP, solubility, MW) from a valid structure. Prediction results are valued and color coded. JRE required.

Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.

Protein informatics site intended to support genomic, proteomic and systems biology research.

"This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease."

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. PubChem collects information on chemical structures, identifiers, chemical and physical properties, biological activities, patents, health, safety, toxicity data, etc. 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 database of known and predicted interactions between chemicals and proteins. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases. The STITCH database covers over 9M proteins from 2031 organisms as of 2021. (EMBL/SIB/CPR-NNF)

A free resource of protein sequence and functional information. (EMBL-EBI, PIR, SIB)

A free database of commercially-available compounds for virtual screening. ZINC contains over 230 million purchasable compounds in ready-to-dock, 3D formats. (UCSF)