1. Home
  2. database

Protein

H-InvDB

noimage
Summary"H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, protein functions, etc."
Data type"RNA human full-length cDNA, mRNA"
Commentary page →

HGPD

noimage
Summary"HGPD is a unique database that stores the information of a set of human Gateway entry clones and protein expression data and helps the user to search the Gateway entry clones. In the full-length human cDNA sequencing project (FLJ project at NEDO), nucleotide sequences of approximately 30000 human cDNA clones have been analyzed.(cited from paper http://nar.oxfordjournals.org/cgi/content/abstract/gkn872?ijkey=zKpNqhZH6jrUuzi&keytype=ref)"
Data typeDNA-sequence
Commentary page →

INOH Pathway Database

noimage
Summary"INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form.(the former URL:http://www.inoh.org/)"
Data typeProtein-Proteome
Commentary page →

LEGENDA

noimage
Summary"Legenda is the system to find articles in which any pair of gene names, diseases, and substrates are co-occurred in the abstract in MEDLINE. Co-occurrence of the same types (e.g. genes) can be searched. Legenda has its own gene name dictionary. "
Data type"Journal , Gene, Disease, Substrate"
Commentary page →

Microorganism database system

noimage
SummaryThis database allows users to search microorganisms and to see the various biological information. This database is available only in Japanese.
Data type"Journal old species name (if any), philogenetic position, type strain, isolation origin, chemical components as chemical taxonomic index, substrate availability, energy gain type, accession number of 16S rDNA to DDBJ/EMBL/GenBank and so on."
Commentary page →

NBRC culture catalogue search

noimage
Summary"Microorganisms (15,400 clones) held by NBRC of NITE can be searched. There are four ways to search, the first is NBRC number, the second is keyword, the third is scientific name or numberof other institutions, and last is homology search. The results can provide the scientific name, history, agency numbers, culture conditions and the paper information. In addition, prokaryotic (16SrDNA) and eukaryotic (28rDNA) for the registration of the sequence to confirm the identity resources search from the search sequence information. (Own translation)"
Data typeDNA-sequence
Commentary page →

PCDq

noimage
Summary"PCDq is a human protein complex database with quality check index (QCI), which describes evidence levels as subunits (protein members) of the protein complex. In total, 1,319 human protein complexes were firstly predicted by finding densely connected regions with cluster properties in the PPI network integrated from six PPI data (BIND, DIP, MINT, HPRD, IntAct, and GNP_Y2H). Then they were curated with the literature so that PCDq consists of both known and predicted complexes/subunits. The evidence level for each subunit were also annotated and summarized to a quality check index (QCI) for each protein complex. PCDq can also show the complicated PPI sub-networks in a simple, editable graphical view ""PPI-Map"". "
Data typeInteraction
Commentary page →

PDB-REPRDB

noimage
Summary"PDB-REPRDB is a reorganized database of protein chains from PDB (Protein Data Bank), and provides 'the list of the representative protein chains' and 'the list of similar protein chain groups'.Chains classified into coiled coil proteins or peptides, according to SCOP, are removed from the database."
Data typeProtein-structure protein chain
Commentary page →

PPI view

noimage
Summary"The PPI view displays H-InvDB human protein-protein interaction (PPI)information. PPI data were collected from five major public PPI databases (BIND, DIP, MINT, HPRD, IntAct) and integrated them as a non-redundant PPI dataset. As the result, we got 32,198 human PPIs comprised of 9,268 proteins. (at H-InvDB version 5.0) The PPI view displays proteins which interact with the usersCHR(39) query proteins (or gene products), and provides links to H-InvDB locus view and cDNA view, which guide you to the gene locations and the detailed gene functional annotations of these interacting proteins, respectively.PPI view: http://www.h-invitational.jp/hinv/ppi/ PPI view sample:http://h-invitational.jp/hinv/ppi/ppi_view.cgi?hip=HIP000084307"
Data typeProtein-Proteome
Commentary page →

ProSeg

noimage
SummaryProSeg is a database of local structures of protein segments. ProSeg contains thousands of clusters of protein segments that were classified according to their three-dimensional structural resemblance.
Data typeProtein-motif
Commentary page →