The National Center for Biotechnology Information ( NCBI)

UniProt: the Universal Protein Resource: UniProt (Universal Protein Resource) is the world's most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.

Brenda:The Comprehensive Enzyme Information System

PDBsum: The PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB).

The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)

SCOPe (Structural Classification of Proteins — extended) is a database developed at the Berkeley Lab and UC Berkeley to extend the development and maintenance of SCOP.

CATH: is a classification of protein structures downloaded from the Protein Data Bank.

TOP: The RCSB Protein Data Bank (PDB): provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease

CSD (The Cambridge Structural Database) – The world's repository for small-molecule crystal structures

CrysMet: The CrystMet database is produced by Toth Information Systems Incorporated, and contains entries covering metals, alloys and intermetallics CrystMet is searchable via the CrystalWorks. Access to the CrystMet database is available both via the CDS/DL server and the Royal Society of Chemistry national CDS site.

ICSD - Inorganic Crystal Structure Database

TOP: ZINC, a free database of commercially-available compounds for virtual screening. ZINC contains over 35 million purchasable compounds in ready-to-dock, 3D formats.

Drug Database: database is a unique 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 8261 drug entries including 2021 FDA-approved small molecule drugs, 233 FDA-approved biotech (protein/peptide) drugs, 94 nutraceuticals and over 6000 experimental drugs. Additionally, 4338 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries.

The Structural Biology Knowledgebase (SBKB) is a free, comprehensive resource that offers a way of keeping abreast of developments both by the PSI and more generally in the fields of structural genomics and structural biology. It is updated weekly to gather the latest structures, models, targets, and annotations from over 100 data sources.

Protein Mutant Database

ProNIT: Database for Protein-Nucleic Acid Interactions: ProNIT database provides experimentally determined thermodynamic interaction data between proteins and nucleic acids

database of three-dimensional protein models calculated by comparative modeling.

DBAli: A Database of Structure Alignments

The Cambridge Structural Database - The world repository of small molecule crystal structures

The National Chemical Database Service: brings together tools and resources for UK researchers in chemistry and related fields.

Database of Macromolecular Movements: This describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural

binding MOAD: We have created a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. Hence, we call it the Mother of All Databases (MOAD).

http://www.ebi.ac.uk/pdbe-site/pdbemotif/

Ensembl Bacteria: Over 20,000 genome sequences from bacteria and archaea.

MicrobesOnline: 3707 genomes, including 1752 bacteria, 94 archaea, and 119 eukaryotes

AMIGO: Search the Gene Ontology database

KEGG: Kyoto Encyclopedia of Genes and Genomes

The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases

Maybridge specialises in producing innovative heterocyclic chemical building blocks for drug discovery chemistry.

ZINC, a free database of commercially-available compounds for virtual screening

DDBJ Center - Japon

MINT database: MINT is a database designed to store functional interactions between biological molecules (proteins, RNA, DNA). Beyond cataloguing the formation of binary complexes, MINT was conceived to store other type of functional interactions namely enzymatic modifications of one of the partners.

list of biological databases