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NIST Chem-BLAST Gateway for PDB

Metadata Updated: July 29, 2022

Chemical Block Layered Alignment of Substructure or Chem-BLAST uses a method for finding chemical compounds within a large collection. In this method, all chemical compounds are annotated in terms of standard chemical structural fragments. These fragments are then organized into a data tree based on their chemical substructures. Search engines have been developed to use this data tree. These search engines use the Chem-BLAST technique to search on the fragments and look for their chemical structural neighbors. The technique was originally developed in the context of the HIV Structural database to enable a query on inhibitors of HIV protease. (See http://xpdb.nist.gov/hivsdb/hivsdb.html.) Recently the method has been significantly improved to extend to the ligands found in the Protein Data Bank (PDB). (See http://xpdb.nist.gov/chemblast/pdb.html.) The method establishes a tree-like relationship between the rings found in three-letter codes that denote ligands of the structures found in the PDB. Semantic Web relations are established between the structural scaffolds of the ligands and organizes them in an XML database utilizing the Web's Resource Description Framework (RDF). An Adobe Flex-based interface is used to present this information on the Web. Plans are under way to extend this work to non-ring type scaffolds as well. Chem-BLAST has also been extended to structures in PubChem. http://xpdb.nist.gov/chemblast/pdb.pl which includes several non-ring standard reused groups such as sulfates. Efforts are under way to use the underlying principles of Chem-BLAST to enable query on non-structural data, such as cell image data http://xpdb.nist.gov/cell/image.pl.

Access & Use Information

Public: This dataset is intended for public access and use. License: See this page for license information.

Downloads & Resources

Dates

Metadata Created Date March 11, 2021
Metadata Updated Date July 29, 2022
Data Update Frequency irregular

Metadata Source

Harvested from NIST

Additional Metadata

Resource Type Dataset
Metadata Created Date March 11, 2021
Metadata Updated Date July 29, 2022
Publisher National Institute of Standards and Technology
Maintainer
Identifier EBC9DB05EDEF5B0EE043065706812DF86
Language en
Data Last Modified 2013-04-01 00:00:00
Category Physics:Thermodynamics, Information Technology:Data and informatics, Bioscience
Public Access Level public
Data Update Frequency irregular
Bureau Code 006:55
Metadata Context https://project-open-data.cio.gov/v1.1/schema/data.json
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id 3622bd6f-2d0b-4938-b4c7-ba5c0e8afb98
Harvest Source Id 74e175d9-66b3-4323-ac98-e2a90eeb93c0
Harvest Source Title NIST
Homepage URL https://data.nist.gov/od/id/EBC9DB05EDEF5B0EE043065706812DF86
License https://www.nist.gov/open/license
Program Code 006:052
Source Datajson Identifier True
Source Hash 792ad5fb4ba3573831c360d3c6318b7dd7857cf6
Source Schema Version 1.1

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