BioTech FYI Center

Structure Databases

4. Structure Databases

4.1. Small molecules

Database name
Full name and/or description
URL
ChEBI
Chemical entities of biological interest
CSD

Cambridge structural database: crystal structure information for organic and metal-organic compounds

HIC-Up
Hetero-compound Information Centre� Uppsala
AANT
Amino acid�nucleotide interaction database
Klotho
Collection and categorization of biological compounds
LIGAND
Chemical compounds and reactions in biological pathways
PDB-Ligand
3D structures of small molecules bound to proteins and nucleic acids
Ligand Depot
Ligand Depot is a data warehouse which integrates databases, services, tools and methods related to small molecules bound to macromolecules.
PubChem
Structures and biological activities of small organic molecules

4.2. Carbohydrates

Database name
Full name and/or description
URL
CCSD
Complex carbohydrate structure database (CarbBank)
CSS

Carbohydrate structure suite: carbohydrate 3D structures derived from the PDB

Glycan
Carbohydrate database, part of the KEGG system
GlycoSuiteDB
N- and O-linked glycan structures and biological sources
Monosaccharide Browser
Space-filling Fischer projections of monosaccharides
SWEET-DB
Annotated carbohydrate structure and substance information

4.3. Nucleic acid structure

Database name
Full name and/or description
URL
NDB
Nucleic acid-containing structures
NTDB
Thermodynamic data for nucleic acids
RNABase
RNA-containing structures from PDB and NDB
SCOR

Structural classification of RNA: RNA motifs by structure, function and tertiary interactions

4.4. Protein structure

Database name
Full name and/or description
URL
ArchDB
Automated classification of protein loop structures
wwPDB
Worldwide Protein Data Bank
PDBj
Protein Data Bank Japan-the archive for macromolecular structures.
ASTRAL

Sequences of domains of known structure, selected subsets and sequence� structure correspondences

BAliBASE
A database for comparison of multiple sequence alignments
BioMagResBank
NMR spectroscopic data for proteins and nucleic acids
CADB
Conformational angles in proteins database
CATH
Protein domain structures database
CE 3D
protein structure alignments
CKAAPs DB
Structurally similar proteins with dissimilar sequences
Dali
Protein fold classification using the Dali search engine
Decoys �R' Us
Computer-generated protein conformations
DisProt

Database of Protein Disorder: proteins that lack fixed 3D structure in their native states

DomIns
Domain insertions in known protein structures
DSDBASE
Native and modeled disulfide bonds in proteins
DSMM
Database of simulated molecular motions
eF-site

Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites

GenDiS
Genomic distribution of protein structural superfamilies
Gene3D
Precalculated structural assignments for whole genomes
GTD
Genomic threading database: structural annotations of complete proteomes
GTOP
Protein fold predictions from genome sequences
Het-PDB
Navi Hetero-atoms in protein structures
HOMSTRAD

Homologous structure alignment database: curated structure-based alignments for protein families

IMB Jena Image Library
Visualization and analysis of 3D biopolymer structures
IMGT/3Dstructure-DB

Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins

ISSD
Integrated sequence�structure database
LPFC
Library of protein family core structures
MMDB
NCBI's database of 3D structures, part of NCBI Entrez
E-MSD
EBI's macromolecular structure database
ModBase
Annotated comparative protein structure models
MolMovDB

Database of macromolecular movements: descriptions of protein and macromolecular motions, including movies

PALI
Phylogeny and alignment of homologous protein structures
PASS2
Structural motifs of protein superfamilies
PepConfDB
A database of peptide conformations
PDB

Protein structure databank: all publicly available 3D structures of proteins and nucleic acids

PDB-REPRDB
Representative protein chains, based on PDB entries
PDBsum
Summaries and analyses of PDB structures
PDB_TM
Transmembrane proteins with known 3D structure
Protein Folding Database
Experimental data on protein folding
SCOP
Structural classification of proteins
Sloop
Classification of protein loops
Structure Superposition Database
Pairwise superposition of TIM-barrel structures
SWISS-MODEL Repository
Database of annotated 3D protein structure models
SUPERFAMILY
Assignments of proteins to structural superfamilies
SURFACE

Surface residues and functions annotated, compared and evaluated: a database of protein surface patches

TargetDB
Target data from worldwide structural genomics projects
3D-GENOMICS
Structural annotations for complete proteomes
TOPS
Topology of protein structures database
Structure Databases