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Structural > Databases

A la mode
A La Mode is an environment for building models of ligand and monomer molecular components. Databases for monomer units and ligands are under construction. A searchable database for the nucleotide units is available.
Biological Macromolecule Crystallization Database Version 4 (BMCD4)
The Biological Macromolecule Crystallization Database Version 4 (BMCD4) compiles crystallization conditions from the literature.
Biological Magnetic Resonance Data Bank (BMRB)
A Repository for Data from NMR Spectroscopy on Proteins, Peptides, and Nucleic Acids.
Biomolecular Object Network Databank (BOND)
Biomolecular Object Network Databank (BOND) is a resource that integrates sequence and interaction information.
CATH is a novel hierarchical classification of protein domains.
The Crystallography Open Database (COD) curently has 48,000 entries.
ChemDB is a public database of small molecules available on the Web. In 2005 the database contained approximately 4.1 million commercially available compounds.
Cryoprotectant database for protein crystals
This web site is a compilation of cryoprotection conditions.
DisProt is a database of proteins that lack fixed 3D structure in their native state.
Disulphide Database (DSDBASE)
DSDBASE is a database on disulphide bonds in proteins.
The DrugBank database combines drug data with drug target information.
GDAP (Genomic Disulfide Analysis Program) provides web access to computationally predicted protein disulfide bonds for over one hundred microbial genomes, including both bacterial and achaeal species.
The Heavy Atom Databank (HAD) is a compilation of conditions used for the preparation of heavy atom derivatives.
HATODAS (Heavy Atom Database System) was designed to help the process of finding useful heavy atom derivatives.
Heavy Atom Reagents Database
Heavy Atom Reagents Database comprises 87 reagents and 30 different heavy atoms.
Hetero-compound Information Centre - Uppsala (HIC-Up)
HIC-Up provides coordinate and dictionary files for most small molecules.
The Inorganic Crystal Structure Database (ICSD) comprises more than 90,000 inorganic structures.
Ligand Depot
Ligand Depot is a data warehouse which integrates databases, services, tools and methods related to small molecules bound to macromolecules.
MERNA is a database of metal ion binding in RNA.
MPCD (Marseille Protein Crystallization Database) combines two crystallization databases, CYCLOP and BMCD (v2.0).
MSD Ligand Chemistry
MSD Ligand Chemistry is a library of ligands, small molecules and monomers that are referred as residues and hetgroups in any PDB entry.
Metalloprotein Database and Browser (MDB)
MDB contains quantitative information on all the metal-containing sites available from structures in the PDB distribution.
NCI open database
NCI open database is a WWW browser to the new and enlarged collection of open NCI database compounds (>250,000 structures).
NDB (Nucleic acid DataBase) is a repository of three-dimesional structural information about nucleic acids.
Pdbfun is a web server for the identification of local structural similarities among annotated residues in proteins.
Protein Data Bank (PDB)
Repository for the processing and distribution of 3-D structural data from biological macromolecules.
Protein Loop Classification
This database of 200+ proteins classifies loops into five types according to their secondary structure.
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.
Reciprocal Net
The Reciprocal Net is a distributed database used by research crystallographers to store information about molecular structures; much of the data is available to the general public.
Refold is a database of refolding protocols for a wide variety of proteins.
Sweet is a program for constructing 3D models of saccharides from their sequences using standard nomenclature.
Structural Classification of Proteins (SCOP)
The SCOP aims to provide a description of the structural and evolutionary relationships between all protein structures.
TargetDB is a protein target registration database. It provides status and tracking information on the progress of the production and solutions of protein structures.
This web site describes various icosahedral virus capsid structures in the Protein Data Bank (PDB) in terms of their complete capsids, detailed structural and computational analysis
ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 4.6 million compounds in ready-to-dock, 3D formats.