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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 http://140.114.100.145/index.html http://www.ncbi.nlm.nih.gov/sites/gquery http://www.ebi.ac.uk/embl/ http://www.uniprot.org/ http://ghr.nlm.nih.gov/
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 ∘ ◎ ∘ ◎  
  ◎: A hyperlink to PDB is provided for a search result.
Gene ontology   GO Taxonomy BioCatalogue
GO
SBO
Taxonomy 		GO
Taxonomy 		 
  Gene Ontology (GO) ∘ ◎ ∘ ∘  
   ◎: 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 ∘ ∘ ∘ ∘  
  ◎: A hyperlink to PubMed of NCBI is provided for a search result.
  1. PRIDE: Proteomics identification database, UniProtKB: UniProt knowledge base of protein sequences, UniRef: UniProt Non-redundant reference databases, UniParc: Non-redundant archive of protein sequences, PDB: Protein database bank, MMDB: The Molecular modeling database, PDBe: Macromolecular structures database, GO: Gene ontology, Taxonomy: NCBI Taxonomy database of organism names, BioCatalogue: BioCatalogue, SBO: Systems biology ontology, KEGG: Kyoto encyclopedia of genes and genomes, Reactome: Database of core biochemical pathways and reactions, BioModels: Database of mathematical models of biological interest, Rhea: Manually annotated database of chemical reactions created in collaboration with the Swiss Institute of Bioinformatics (SIB), PubMed: PubMed of NCBI, Medline: Citations and abstracts from many life-science journals, Patents: Biology-related abstracts of patent applications.
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BMC Bioinformatics

ISSN: 1471-2105

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