Table 1 A comparison for database contents and searching functions provided by HDAPD with those provided by databases NCBI Entrez, EMBL, UniProt, and GHR
From: HDAPD: a web tool for searching the disease-associated protein structures
Databases | HDAPD | NCBI Entrez | EMBL | UniProt | GHR | |
|---|---|---|---|---|---|---|
Web site | ||||||
Functions | Disease types | ICD-10; Genes and Disease (classified diseases into 14 groups; 285 diseases) | (classified diseases into 17 groups) | |||
Disease list | ∘ | ∘ | ||||
Disease introduction | Gene Review; Genetics Home Reference | |||||
Disease introduction | ∘ | ∘ | ∘ | |||
Disease-associated proteins | ICD-10; Genes and Disease; OMIM | |||||
Disease-associated protein list | ∘ | * | * | * | ||
*A protein list is provided by typing in keywords. | ||||||
Determine-d and annotated protein sequences | SwissProt, PIR, PRF, PDB, | PRIDE UniProtKB UniRef UniParc | UniProtKB UniRef UniParc | |||
Sequence database | ∘ | ∘ | ∘ | |||
Determine-d protein structure | 3-D macromolecular structures | PDB (3,189 all are diseases-associated) | MMDB (over 20000 structures, but not disease-associated) | PDBe | PDB PDBe | |
PDB ID | ∘ | ∘ | ∘ | ∘ | ||
Compound | ∘ | ∘ | ∘ | ◎ | ||
Classification | ∘ | ∘ | ∘ | ◎ | ||
Source | ∘ | ◎ | ∘ | ◎ | ||
Resolution | ∘ | ◎ | ∘ | ∘ | ||
Method | ∘ | ◎ | ∘ | ∘ | ||
Author List | ∘ | ∘ | ∘ | ◎ | ||
Accession Date | ∘ | ∘ | ∘ | ◎ | ||
Protein sequence (Primary) | ∘ | ∘ | ∘ | ◎ | ||
Molecular viewer | ∘ | ◎ | ∘ | ◎ | ||
â—Ž: A hyperlink to PDB is provided for a search result. | ||||||
Gene ontology | GO | Taxonomy | BioCatalogue GO SBO Taxonomy | GO Taxonomy | ||
Gene Ontology (GO) | ∘ | ◎ | ∘ | ∘ | ||
â—Ž: A hyperlink to PubMed of NCBI is provided for a search result. | ||||||
Pathway | Pathway and systems of interacting molecules | KEGG | KEGG Reactome | BioModels Reactome Rhea | UniProtKB/Swiss-Prot | |
Pathway description | ∘ | ∘ | ∘ | ∘ | ||
Pathway map | ∘ | ∘ | ∘ | ∘ | ||
Literature | Full text and journal articles | PubMed | PubMed | Medline Patents | PubMed SRS CiteXplore | PubMed |
Literature extracting | ∘ | ∘ | ∘ | ∘ | ||
Author | ∘ | ∘ | ∘ | ∘ | ◎ | |
Journal | ∘ | ∘ | ∘ | ∘ | ◎ | |
Relative date | ∘ | ∘ | ∘ | ∘ | ◎ | |
Sorting | ∘ | |||||
Date | ∘ | ∘ | ∘ | ∘ | ||
â—Ž: A hyperlink to PubMed of NCBI is provided for a search result. | ||||||