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PoSSuM: Pocket Similarity Search using Multiple-Sketches

IDNBDC common database IDs, which should be written in parentheses if there are multiple titles, such as Japanese and English. NBDC01144
Database nameName of the database PoSSuM
Alternative nameAlternative name of the database Pocket Similarity Search using Multiple-Sketches
URLURL of the database http://possum.cbrc.jp/PoSSuM/
Database maintenance siteSite maintaining the database AIST (National Institute of Advanced Industrial Science and Technology) (Link to J-Global)
Country/RegionCountry or region name where the database maintenance site is located Japan
Database descriptionDatabase descirption This site contains a database of protein-ligand binding sites that have been compared and numbered according to resemblance in structure. Comparing the huge amounts of small molecule binding sites of proteins available in the PDB (Protein Data Bank) is important in order to determine anticipated protein functions, the knowledge of which may then be applied in the research and discovery of new drugs. The software program used, "SketchSort", proved to be an extremely fast method. All-pair similarity searches were done for 3.4 million binding sites and over 24 million analogous pairs were found. The results, presented as a PoSSuM (Pocket Similarity Search using Multiple-Sketches) database contain all pairs identified and include commentary notes of various types, namely CATH (protein structure classification according to Class, Architecture, Topology and Homologous superfamily), SCOP (Structural Classification of Proteins), EC number (Enzyme Commission number) and gene ontology. Two search modes are provided: Search K, to find analogous binding sites to a familiar ligand-binding site entered and Search P, to predict ligands that show potential to bind to a protein structure entered.
Organism(s) coveredNCBI Taxonomy names and IDs covered by the database ―
Tag - TargetTag to indicate targets for this database such as genome and protein
Genome/Gene
cDNA/EST
Genetic variation
Epigenetics
DNA
RNA
Protein
Carbohydrate
Lipid
Metabolite
Chemical compound
Drug
Cell/Organelle
Organism
Health/Disease
Tag - Information typeTag to indicate information types for this database such as sequence and structure
Phenotype
Bioresource
Method
Ontology/Terminology/Nomenclature
Environment
Sequence
3D structure
Chemical structure
Expression
Localization
Geographic Distribution
Interaction/Pathway
Taxonomy
Classification
Image/Movie
Bibliography/Documents
Portal
Repository
Reference(s) - PubMed ID/DOIPubMed IDs/DOI for papers related to the database
PubMed ID:22135290
DOI:-
Language(s)Languages in which the contents of the database are displayed English
Operational statusOperational status for the database Inactive
Link(s) to Downloadable dataLinks to downloadable data https://dbarchive.biosciencedbc.jp/en/possum/download.html
Link(s) to MetaData of downloadable dataLinks to metadata of downloadable data https://dbarchive.biosciencedbc.jp/data/possum/LATEST/README_e.html
Link(s) to Terms of useLinks to terms of use of downloadable data https://dbarchive.biosciencedbc.jp/en/possum/lic.html
Link(s) to "How to use" ―
Contact information of database ―
Link(s) to API / SPARQL endpoint ―
Link to LSDB ArchiveLink to LSDB Archive https://dbarchive.biosciencedbc.jp/en/possum/desc.html
Link to MEDALS Database listLink to MEDALS Database list http://medals.jp/elist/detail/175.html
Link to TogoTVLink to TogoTV ―
Link to FAIRsharingLink to FAIRsharing https://fairsharing.org/biodbcore-000127
Similar databasesDatabases that are similar to this database.
Record maintainerRecord maintainer Integbio Database Catalog
Record sourceOrganization that originally created the record
Date of creation of this recordDate of creation of this English record 2013-06-17
Last update date of this recordLast update date of this English record 2022-01-16
Record license Creative Commons CC0 license