Structure Data Format
How to cite this record FAIRsharing.org: SDF; Structure Data Format; DOI: https://doi.org/10.25504/FAIRsharing.ew26v7; Last edited: Jan. 8, 2019, 1:35 p.m.; Last accessed: Feb 21 2020 11:48 p.m.
Record updated: July 17, 2018, 11:10 a.m. by The FAIRsharing Team.
Edits to 'https://fairsharing.org/FAIRsharing.ew26v7' by 'The FAIRsharing Team' at 11:10, 17 Jul 2018 (approved): 'domains' has been modified: Before: Life Science|domain|http://www.fairsharing.org/ontology/SRAO_0000069 Molecular entity|material|http://purl.obolibrary.org/obo/CHEBI_23367 Molecular structure|information content entity|http://edamontology.org/data_0883 X-ray crystallography assay|process|http://purl.obolibrary.org/obo/OBI_0000912 After: Life Science|domain|http://www.fairsharing.org/ontology/SRAO_0000069 Molecular entity|material|http://purl.obolibrary.org/obo/CHEBI_23367 Molecular structure|information content entity|http://edamontology.org/data_0883 X-ray crystallography assay|process|http://purl.obolibrary.org/obo/OBI_0000912 Chemistry|process|http://edamontology.org/topic_3314 Added: Chemistry|process|http://edamontology.org/topic_3314 Removed:
Edits to 'https://fairsharing.org/FAIRsharing.ew26v7' by 'The FAIRsharing Team' at 11:03, 17 Jul 2018 (approved): 'miriam_url' has been modified: Before: None After:
Edits to 'https://fairsharing.org/FAIRsharing.ew26v7' by 'The FAIRsharing Team' at 22:04, 23 Oct 2016 (approved): 'shortname' has been modified: Before: Structure Data Format After: SDF
No XSD schemas defined
Conditions of Use
Description of several chemical-structure file formats used by computer-programs developed at Molecular Design Limited
Dalby A, Nourse JG, Hounshell WD, Gushurst Aki, Grier DL, Leland BA, Laufer J
Journal of Chemical Information and Computer Sciences 1992
No guidelines defined
No semantic standards defined
Models and Formats
No identifier schema standards defined
No metrics standards defined
BitterDB is a free and searchable database of bitter compounds. Compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste re- ceptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness.
canSAR is an integrated cancer research and drug discovery resource that brings together large-scale data from different disciplines and allows query and exploration to help cancer research and drug discovery.
Protein-Chemical Structural Interactions
Protein-Chemical Structural Interactions provides information on the 3-dimensional chemical structures of protein interactions with low molecular weight.
Rhea is a comprehensive and non-redundant resource of expert-curated chemical and transport reactions of biological interest. Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. Rhea describes enzyme-catalyzed reactions covering the IUBMB Enzyme Nomenclature list as well as additional reactions, including spontaneously occurring reactions. Rhea is built on ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to describe its reaction participants. Since December 2018, Rhea is the standard for enzyme annotation in UniProt.
SCRIPDB: A Portal for Easy Access to Syntheses, Chemicals, and Reactions In Patents
SCRIPDB is a chemical structure database designed to make patent metadata accessible. We index public-domain chemical information contained in U.S. patents, and provide the full patent text, reactions, and relationships described within any individual patent, as well as the original CDX, MOL, and TIFF files.
TTD, Therapeutic Target Database
The Therapeutic Target Database provides information about therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information is fully referenced.
The Yeast Metabolome DataBase
The Yeast Metabolome Database (YMDB) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae (also known as Baker’s yeast and Brewer’s yeast). This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases.
The DrugBank database is a freely available bioinformatics and chemoinformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
Chemical Component Dictionary
The Chemical Component Dictionary is an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names.
Drug Adverse Reaction Target
A database for facilitating the search for drug adverse reaction target. DART contains information about known drug adverse reaction targets, functions and properties.
ChemSpider is a freely available collection of compound data from across the web, which aggregates chemical structures and their associated information into a single searchable repository entry. These entries are supplemented with additional properties, related information and links back to original data sources.
PathBank is an interactive, visual database containing more than 100 000 machine-readable pathways found in model organisms such as humans, mice, E. coli, yeast, and Arabidopsis thaliana. The majority of these pathways are not found in any other pathway database. PathBank is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics, and systems biology. All PathBank pathways include information on the relevant organelles, subcellular compartments, protein complex cofactors, protein complex locations, metabolite locations, chemical structures, and protein complex quaternary structures. The database is easily browsed and supports full text, sequence, and chemical structure searching.
Scroll for more...
This record is not implemented by any policy.
This record is in need of a maintainer. If you login, you'll be able to claim this record.
MDL Information Systems (Consortium)