Macromolecule Structure Databases

Primary Databases of Empirically Determined 3-D Models
open in new windowBMRB	BioMagResBank. A repository for data from NMR spectroscopy on biomolecules. The BMRB is part of the wwPDB. The coordinates and constraint data is released by the PDB while other NMR spectral data (such as chemical shifts, coupling constants, and relaxation parameters) is archived by BMRB.
open in new windowCSD	The Cambridge Structural Database. Commercial repository of small organic molecule crystal structures including short polypeptides and polysaccharides (WIS licensed CSD)
open in new windowNDB	A repository of structural information about nucleic acids. The structures are archived both in the wwPDB and in the NDB.
open in new windowwwPDB	The worldwide Protein Data Bank (wwPDB) is the internationally recognized single repository of all published macromolecular three-dimensional structures determined empirically. The PDB archive can be accessed via the following portals: open in new windowRCSB PDB (USA) MSD-EBI (Europe) open in new windowPDBj (Japan)
Alerts
	open in new windowPDBalert	Automatic system that alerts users as soon as a PDB structure with homology to a protein of interest becomes available
	soaPDB	Web tool for generation and organization of saved PDB searches, including automatic email alerts
	open in new windowSeqAlert	Automatic system that alerts users as soon as a PDB structure with homology to a protein of interest becomes available

Related (derived) Structural Databases
Jena Library	The database aim to integrate information regarding structural models in the PDB with an emphasis on visualization and analysis.
open in new windowMMDB	NCBI's Entrez 3-D structure database. The NCBI has cross-linked structural data to bibliographic information, to the sequence databases, and to the NCBI taxonomy. It include tools for sequence and structure visualization (Cn3D).
open in new windowOCA	OCA, a browser-database for protein structure/function. OCA integrates data from several open in new windowsources with an emphasis on sequence-structure-function information.
open in new windowPDBsum	The PDBsum is a pictorial database that provides an at-a-glance overview of the contents of each 3D structure deposited in the PDB. It shows the molecule(s) that make up the structure (i.e. protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions.
PDBWiki	Community annotated knowledge base of biological molecular structures and related information.
open in new windowProteopedia	Collaborative wiki encyclopedia of proteins and other macromolecules structures. Proteopedia contains a page for every entry in the wwPDB, as well as users made interactive pages that are aimed to present structure/function information in a user-friendly manner to a broad scientific audience. Proteopedia employs an easy-to-use scene-authoring tool.

Structural Classification Databases
CATH	Hierarchical classification database
open in new windowSCOP	Hierarchical classification database
open in new windowThe Dali Database	Fold classification based on structure-structure alignment of proteins
TOPS	Protein topologies database

Specialized Structural Databases

The following databases focused on specific protein families or other biological macromolecules and include structural information derived from the wwPDB.
open in new windowAmyPDB	Amyloid proteins,
open in new windowAntibodies	Cytochrome P450
open in new windowCAZy	Carbohydrate active enzymes
CyBase	Cyclic proteins
open in new windowCYPED
open in new windowEC→PDB	Enzymes
open in new windowESTHER	Alpha/beta hydrolases homologous to cholinesterases
open in new windowEyeSite	Proteins that function in the eye
open in new windowGLYCO3D	Carbohydrates, Lectines, Glycosyltransferases, Gag binding proteins
GlycoSuite	Glycans
glycoSCIENCE
open in new windowGPCRDB	G protein-coupled receptors
open in new windowHIV Structural Database
open in new windowHMPDb	Human mitochondrial proteins
open in new windowHmrbase	Hormones
open in new windowHomeodomain Resource
open in new windowKNOTIN
open in new windowLS-SNP/PDB	Annotated non-synonymous SNPs mapped to PDB structures
MEROPS	Peptidases
MDB	Metalloproteins
MemPro	Membrane proteins
MPDB	Membrane proteins
RNA FRABASE
SAAPdb	Mapping SNPs and pathogenic deviations (PDs) to protein structural data
SDAP	Allergenic proteins
EF-Hand

Databases of Theoretically Determined 3-D Models

The following databases include 3-D models of proteins calculated by comparative modeling. Before you start your own comparative modeling project, try these databases.
open in new windowMODBASE	Automatic calculations with ModPipe
open in new windowPMP	Models structures from different resources (CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, ModBase, SWISS-MODEL Repository)
open in new windowSWISS MODEL Repository	Automatic calculations with SWISS_MODEL

Primary Databases of Empirically Determined 3-D Models