HOME Help Statistics Acknowledgement Developers Contact

Links to Databases

Links on this page provide information on various databases in the filed of protein structure.

Name of databases            Description  Reference  URL  Download
PDBProtein Data Bank (PDB) is a archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.PMID:18156675Protein Data Bank (PDB)Structure Download
PDBsumPDBsum is a database of mainly pictorial summaries of the 3D structures of proteins and nucleic acids in the Protein Data Bank. PMID:15608193PDBsumPDBsum
PDBFINDERThe PDBFINDER database provides an easy to interpret file containing summary information about all Protein Data Bank files.PMID:9021272PDBFINDERFTP-PDBFINDER
DSSPDSSP is a Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.PMID:6667333DSSPDSSP
PFAMPfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.PUBMED:19920124Pfam Pfam database
PISCESPISCES is a database of PDB derived Datasets with non-redundant sequence and structural quality criteria.PMID:12912846PISCESPISCES database
HSSPThe HSSP database is a database of homology-derived secondary structure of proteins.PMID:8594579HSSPHSSP database
PDIDBPDIdb (Protein-DNA Interface database) is a repository containing relevant structural information of Protein-DNA complexes solved by X-Ray cristallography and available at the Protein Data Bank (PDB).PMID:20482798PDIdb (Protein-DNA Interface database)Download PDIdb
SCOPThe Structural Classification of Proteins (SCOP) database is a manual classification of protein structural domains for the investigation of sequences and structures.PMID:7723011SCOP: Structural Classification of Proteins.SCOP database
CATHCATH is a manually curated classification of protein domain structures.PMID:20368142CATH:protein structure classificationCATH Data
PCDBPCDB is a database of protein conformational diversity. For each protein, the database contains the redundant compilation of all the corresponding crystallographic structures obtained under different conditions.PMID:21097895PCDB: a database of protein conformational diversity.PCDB Search
OCAOCA is a browser-database for protein structure/function.Jaime PriluskyOCAOCA data search
PDBeProtein Data Bank in Europe (PDBe) is the the collection, management and distribution of data about macromolecular structures, derived from the Protein Data Bank (PDB).PMID:21460450PDBe: Protein Data Bank in EuropePDBe
MMDBIt is annotating protein sequences with Entrez's 3D-structure database.PMID:17135201Molecular Modeling Database (MMDB)Search Structure
fireDBfireDB is a database of PDB structures and their associated ligands.PMID:17132832FireDBSearch the database
SCOPOI It is a database of all domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions.PMID:16381874SCOPPISearch entries
DIPDatbase of Interacting Proteins (DIP) is a database of experimentally determined interactions between proteins.PMID:14681454 DIP: Datbase of Interacting ProteinsDIP SEARCH
PDB_REDOA databank with updated and optimised macromolecular X-ray diffraction structure models.PMC3013697PDB_REDOPDB_REDO
Het-PDB NaviDatabase contains 4,189 types of small molecules that interact with proteinsPMID14999012Het-PDB NaviSearch and Download
Ligand ExpoLigand Expo includes chemical descriptions for about 4600 small molecules that are part of the structures deposited with the PDB.PMID15059838Ligand ExpoLigand Expo
SuperSiteThe main data is made up of 8000 metabolites including 1300 drugs, bound to about 290,000 different receptor binding sites.PMID18842629SuperSiteSuperSite
PDB-LigandCurrently, PDB-Ligand holds 4870 different types of ligands, extracted from 116,019 ligand-binding structures derived from about 25 000 PDB entries. PMID15608186PDB-LigandPDB-Ligand
SuperLigandsSuperLigands is an encyclopedia that is dedicated to a ligand oriented view of the protein structural space: it contains 10085 different ligands and 401300 total number of instances in PDB files.PMID15943884SuperLigandsSuperLigands
Binding MOADBinding MOAD currently contains: 13,138 Protein-Ligand Structures, 4,146 Structures with Binding Data, 6,210 Different Ligands.PMID18055497Binding MOADBinding MOAD
PLIDProtein Ligand Interaction (PLID): contains 6295 ligands bound to proteins extracted from the protein data bank (PDB).PMID18514578PLIDPLID
sc-PDBt contains 8187 entries, 2638 proteins and 4231 ligands.PMID16563002sc-PDBsc-PDB
AffinDBAffinDB currently contains over 730 affinity entries covering more than 450 different protein-ligand complexes.PMID16381925AffinDBAffinDB
ChEMBLdb ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).PMID19194660ChEMBLdbSearch ChEMBLdb
KEGGKEGG: Kyoto EncyclopediaPMID18077471 KEGG LIGAND DatabaseLIGAND Database
HMDB The Human Metabolome Database (HMDB) PMID18953024HMDBHMDB
SMPDB Small Molecule Pathway Database (SMPDB)PMID19948758SMPDBSMPDB
DrugBank DrugBank: contains nearly 4800 drug entries including >1,350 FDA-approved small molecule drugs, 123 FDA approved biotech (protein/peptide) drugs, 71 nutraceuticals and >3,243 experimental drugs.PMID18048412DrugBankDrugBank
PubChem PubChem is a database of chemical molecules, maintained by the National Center for Biotechnology Information (NCBI).PubChemPubChemPubChem
TTD Therapeutic Target Database (TTD)includes information about 348 successful, 292 clinical trial and 1254 research targets, 1514 approved, 1212 clinical trial and 2302 experimental drugs linked to their primary targets (3382 small molecule and 649 antisense drugs with available structure and sequence) PMID19933260TTDTTD
T3DB Toxin and Toxin Target Database (T3DB): Currently houses over 2900 toxins described by over 34 200 synonyms, including pollutants, pesticides, drugs, and food toxins.PMID19897546T3DBT3DB