Structural Databases 
Structural Databases
Nucleic acid structure
|
Database name
|
Description
|
|
Nucleic acid-containing structures
|
|
|
Thermodynamic data for nucleic acids
|
|
|
RNA-containing structures from PDB and NDB
|
|
|
Structural classification of RNA: RNA motifs by structure, function and tertiary interactions |
Protein structure
| Database name | Description |
|
Automated classification of protein loop structures |
|
|
Sequences of domains of known structure, selected subsets and sequence-structure correspondences |
|
|
A database for comparison of multiple sequence alignments |
|
|
NMR spectroscopic data for proteins and nucleic acids |
|
|
Conformational angles in proteins database |
|
|
Protein domain structures database |
|
|
3D protein structure alignments |
|
|
Structurally-similar proteins with dissimilar sequences |
|
|
Conservation of conservation: Universally conserved residues in selected protein folds |
|
|
Annotation of protein structures from the PDB |
|
|
Protein fold classification using the Dali search engine |
|
|
Computer-generated protein conformations |
|
|
Database of Protein Disorder: proteins that lack fixed 3D structure in their native states |
|
|
A database of multiple alignments for protein structures |
|
|
Domain insertions in known protein structures |
|
|
Native and modeled disulfide bonds in proteins |
|
|
Database of simulated molecular motions |
|
|
Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites |
|
|
Flexible structural neighborhood, structural neighbors of proteins identified by FATCAT tool |
|
|
Genomic distribution of protein structural superfamilies |
|
|
Precalculated structural assignments for whole genomes |
|
|
Genomic threading database: Structural annotations of complete proteomes |
|
|
Protein fold predictions from genome sequences |
|
|
Hetero-atoms in protein structures |
|
|
Homologous structure alignment database: curated structure-based alignments for protein families |
|
|
Visualization and analysis of 3D biopolymer structures |
|
|
Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins |
|
|
Spatially interacting motif database |
|
|
Integrated sequence-structure database |
|
|
Library of protein family core structures |
|
|
NCBI’s database of 3D structures, part of NCBI Entrez |
|
|
EBI’s macromolecular structure database |
|
|
Annotated comparative protein structure models |
|
|
Database of macromolecular movements: Descriptions of protein and macromolecular motions, including movies |
|
|
Phylogeny and alignment of homologous protein structures |
|
|
Structural motifs of protein superfamilies |
|
|
A database of peptide conformations |
|
|
Protein structure databank: all publicly available 3D structures of proteins and nucleic acids |
|
|
Representative protein chains, based on PDB entries |
|
|
Summaries and analyses of PDB structures |
|
|
Transmembrane proteins with known 3D structure |
|
|
3D protein models obtained from structure predictions |
|
|
Experimental data on protein folding |
|
|
Structural classification of proteins |
|
|
Structural classification of protein-protein interfaces |
|
|
Classification of protein loops |
|
|
Amino acid properties in proteins of known structure |
|
|
Pairwise superposition of TIM-barrel structures |
|
|
Assignments of proteins to structural superfamilies |
|
|
Surface residues and functions annotated, compared and evaluated: a database of protein surface patches |
|
|
Database of annotated 3D protein structure models |
|
|
Target data from worldwide structural genomics projects |
|
|
Structural annotations for complete proteomes |
|
|
Topology of protein structures database |
Small molecules
|
Database name
|
Description
|
|
Chemical entities of biological interest
|
|
|
Cambridge structural database: crystal structure information for organic and metal-organic compounds |
|
|
Hetero-compound Information Centre— Uppsala
|
|
|
Amino acid–nucleotide interaction database
|
|
|
Collection and categorization of biological compounds
|
|
|
Chemical compounds and reactions in biological pathways
|
|
|
3 D structures of small molecules bound to proteins and nucleic acids
|
|
|
Ligand Depot is a data warehouse which integrates databases, services,
tools and methods related to small molecules bound to macromolecules.
|
|
|
Structures and biological activities of small organic molecules
|
Carbohydrates
|
Database name
|
Description
|
|
Complex carbohydrate structure database (CarbBank)
|
|
|
Carbohydrate structure suite: carbohydrate 3D structures derived from the PDB |
|
|
Carbohydrate database, part of the KEGG system
|
|
|
N- and O-linked glycan structures and biological sources
|
|
|
Space-filling Fischer projections of monosaccharides
|
|
|
Annotated carbohydrate structure and substance information
|