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
CATH is a novel hierarchical classification of protein domains. |
COD
The Crystallography Open Database (COD) curently has 48,000 entries. |
ChemDB
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
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. |
DrugBank
The DrugBank database combines drug data with drug target information. |
GDAP
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. |
HAD
The Heavy Atom Databank (HAD) is a compilation of conditions used for the preparation of heavy atom derivatives. |
HATODAS
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. |
ICSD
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
MERNA is a database of metal ion binding in RNA. |
MPCD
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
NDB (Nucleic acid DataBase) is a repository of three-dimesional structural information about nucleic acids. |
Pdbfun
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. |
RESID
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
Refold is a database of refolding protocols for a wide variety of proteins. |
SWEET
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
TargetDB is a protein target registration database. It provides status and tracking information on the progress of the production and solutions of protein structures. |
VIPERdb
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
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. |