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

The SCOP (Structural Classification of Proteins) database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.

CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).

Protein Structure Database in Europe, a project for the collection, management and distribution of data about macromolecular structures, derived from the Protein Data Bank (PDB).

The Molecular Modeling Database (MMDB) contains 3D macromolecular structures, including proteins and polynucleotides. MMDB contains over 40,000 structures and is linked to the rest of the NCBI databases.

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

This database contains the known enzyme structures that have been deposited in the Protein Data Bank (PDB).

Nucleic Acid Database - a repository of three-dimensional structural information about nucleic acids.

Relibase is a database search, retrieval and analysis system for protein-ligand complex structures. Relibase+ provides easy access to all such experimental structures within the Protein Data Bank (PDB)

A database of ligand binding proteins aligned to structural templates. The structural templates are taken from the PDB  , 3D models of the aligned sequences are provided ModBase, and pairwise sequence alignments are provided by CE. Multiple Structural Alignments are built on the fly within LigBase from a series of pairwise alignments.

Ligand Protein Database

A Comprehensive Database of Structurally Defined Interfaces in Proteins

A Database of Structure Alignments.

ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 8 million purchasable compounds in ready-to-dock, 3D formats.

BMRB's mission is to collect, archive, and disseminate the important quantitative data derived from NMR spectroscopic investigations of biological macromolecules.

The Jena Library of Biological Macromolecules (JenaLib) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization and analysis.

KEGG LIGAND contains our knowledge on the universe of chemical substances and reactions that are relevant to life. It is a composite database currently consisting of COMPOUND, DRUG, GLYCAN, REACTION, RPAIR, and ENZYME databases.

A database containing over four million small organic compounds @ UC Irvine.

Empirical and theoretical structures for more than 18,000 inorganic crystals and small organic compounds.