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 |
| PDB | Protein Data Bank (PDB) is a archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. | PMID:18156675 | Protein Data Bank (PDB) | Structure Download |
| PDBsum | PDBsum is a database of mainly pictorial summaries of the 3D structures of proteins and nucleic acids in the Protein Data Bank. | PMID:15608193 | PDBsum | PDBsum |
| PDBFINDER | The PDBFINDER database provides an easy to interpret file containing summary information about all Protein Data Bank files. | PMID:9021272 | PDBFINDER | FTP-PDBFINDER |
| DSSP | DSSP is a Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. | PMID:6667333 | DSSP | DSSP |
| PFAM | Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. | PUBMED:19920124 | Pfam | Pfam database |
| PISCES | PISCES is a database of PDB derived Datasets with non-redundant sequence and structural quality criteria. | PMID:12912846 | PISCES | PISCES database |
| HSSP | The HSSP database is a database of homology-derived secondary structure of proteins. | PMID:8594579 | HSSP | HSSP database |
| PDIDB | PDIdb (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:20482798 | PDIdb (Protein-DNA Interface database) | Download PDIdb |
| SCOP2 | The Structural Classification of Proteins (SCOP2) database is a manual classification of protein structural domains for the investigation of sequences and structures. | PMID:24293656 | SCOP2 | SCOP2 database |
| CATH | CATH is a manually curated classification of protein domain structures. | PMID:20368142 | CATH:protein structure classification | CATH Data |
| PCDB | PCDB 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:21097895 | PCDB: a database of protein conformational diversity. | PCDB Search |
| OCA | OCA is a browser-database for protein structure/function. | Jaime Prilusky | OCA | OCA data search |
| PDBe | Protein 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:21460450 | PDBe: Protein Data Bank in Europe | PDBe |
| MMDB | It is annotating protein sequences with Entrez's 3D-structure database. | PMID:17135201 | Molecular Modeling Database (MMDB) | Search Structure |
| fireDB | fireDB is a database of PDB structures and their associated ligands. | PMID:17132832 | FireDB | Search 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:16381874 | SCOPPI | Search entries |
| DIP | Datbase of Interacting Proteins (DIP) is a database of experimentally determined interactions between proteins. | PMID:14681454 | DIP: Datbase of Interacting Proteins | DIP SEARCH |
| PDB_REDO | A databank with updated and optimised macromolecular X-ray diffraction structure models. | PMC3013697 | PDB_REDO | PDB_REDO |
| Het-PDB Navi | Database contains 4,189 types of small molecules that interact with proteins | PMID14999012 | Het-PDB Navi | Search and Download |
| Ligand Expo | Ligand Expo includes chemical descriptions for about 4600 small molecules that are part of the structures deposited with the PDB. | PMID15059838 | Ligand Expo | Ligand Expo |
| SuperSite | The main data is made up of 8000 metabolites including 1300 drugs, bound to about 290,000 different receptor binding sites. | PMID18842629 | SuperSite | SuperSite |
| PDB-Ligand | Currently, PDB-Ligand holds 4870 different types of ligands, extracted from 116,019 ligand-binding structures derived from about 25 000 PDB entries. | PMID15608186 | PDB-Ligand | PDB-Ligand |
| SuperLigands | SuperLigands 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. | PMID15943884 | SuperLigands | SuperLigands |
| Binding MOAD | Binding MOAD currently contains: 13,138 Protein-Ligand Structures, 4,146 Structures with Binding Data, 6,210 Different Ligands. | PMID18055497 | Binding MOAD | Binding MOAD |
| PLID | Protein Ligand Interaction (PLID): contains 6295 ligands bound to proteins extracted from the protein data bank (PDB). | PMID18514578 | PLID | PLID |
| sc-PDB | t contains 8187 entries, 2638 proteins and 4231 ligands. | PMID16563002 | sc-PDB | sc-PDB |
| AffinDB | AffinDB currently contains over 730 affinity entries covering more than 450 different protein-ligand complexes. | PMID16381925 | AffinDB | AffinDB |
| 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). | PMID19194660 | ChEMBLdb | Search ChEMBLdb |
| KEGG | KEGG: Kyoto Encyclopedia | PMID18077471 | KEGG LIGAND Database | LIGAND Database |
| HMDB | The Human Metabolome Database (HMDB) | PMID18953024 | HMDB | HMDB |
| SMPDB | Small Molecule Pathway Database (SMPDB) | PMID19948758 | SMPDB | SMPDB |
| 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. | PMID18048412 | DrugBank | DrugBank |
| PubChem | PubChem is a database of chemical molecules, maintained by the National Center for Biotechnology Information (NCBI). | PubChem | PubChem | PubChem |
| 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) | PMID19933260 | TTD | TTD |
| 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. | PMID19897546 | T3DB | T3DB |
| BMRB | BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. | PMID17984079 | BMRB | FTP-BMRB |
| ModBase | MODBASE is a queryable database of annotated protein structure models. The models are derived by ModPipe, an automated modeling pipeline relying on the programs PSI-BLAST and MODELLER. MODBASE contains theoretically calculated models, which may contain significant errors, not experimentally determined structures. | PMID24271400 | ModBase | FTP-ModBase |
| SWISS-MODEL Repository (SMR) | SWISS-MODEL Repository (SMR) is a database of annotated 3D protein structure models generated by the automated SWISS-MODEL homology modeling pipeline. It currently holds >400 000 high quality models covering almost 20% of Swiss-Prot/UniProtKB entries. | PMID27899672 | SWISS-MODEL Respository | SWISS-MODEL Repository |
Links on this page provide information on various databases in the filed of protein protein interactions
| Name of databases | Description | Reference | URL | Download |
| APID | APID (Agile Protein Interactomes DataServer) provides a comprehensive collection of protein interactomes for more than 400 organisms based in the integration of known experimentally validated protein-protein physical interactions. | PMID27131791 | APID | APID |
| BioGRID3.4 | The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans. BioGRID currently holds over 1,400,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 57,000 publications in the primary literature. | PMID27980099 | BioGRID | BioGRID |
| 3did | The database of three-dimensional interacting domains (3did) is a collection of high-resolution three-dimensional structural templates for domain-domain interactions. It contains templates for interactions between two globular domains as well as novel domain-peptide interactions. | PMID20965963 | 3did | 3did |
| DIP | The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. | PMID14681454 | DIP | DIP |
| PiSITE | PiSITE is a web-based database of protein interaction sites. The PiSITE provides information of interaction sites of a protein from single PDB entry and information of interaction sites of a protein from multiple PDB entries including similar proteins.This provides real interaction sites of proteins using the complex structures in PDB. | PMID18836195 | PiSITE | PiSITE |
| DOMMINO2.0 | DOMMINO2.0 is a comprehensive structural database on macromolecular interactions.It has the capability to study macromolecular interactions in a PDB structure at the interaction network level and at the individual interface level. | PMID26827237 | DOMMINO2.0 | DOMMINO2.0 |
| IID | IID (Integrated Interaction Database) is an on-line database of known and predicted eukaryotic protein-protein interactions, in 30 tissues of model organisms and humans. | PMID26516188 | IID | IID |
| STRING | STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases. | PMID27924014 | STRING | STRING |
| MIPS | The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions. | PMID15531608 | MIPS | MIPS |
| UniHi | Unified Human Interactome (UniHI) is a database for retrieval, analysis and visualization of human molecular interaction networks. Its primary aim is to provide a comprehensive and easy-to-use platform for network-based investigations to a wide community of researchers in biology and medicine. | PMID24214987 | UniHi | UniHi |