![]() ![]() In PubChem, records are retrieved based on a Tanimoto threshold. Each compound pair receives a Tanimoto (or Jaccard) score. When a structure search is initiated the query structure's fingerprint is compared to each of PubChem Compound structure fingerprints and a similarity value is calculated from the Tanimoto (or Jaccard) equation. (Please note: The fingerprint does not consider variation in stereochemical or isotopic information.) Collectively, these binary keys provide a "fingerprint" of a particular chemical structure valence-bond form. Each key denotes the presence or absence of a particular substructure in a molecule. PubChem Compound structures are mapped onto this dictionary to create for each a fingerprint of chemical substructure "keys". PubChem has a binary fingerprint dictionary of 81 different chemical structure fragments. Creating assays to differentiate and identify key compounds in environmental samples.Ordering sets of compounds for doing biochemical or cellular bioactivity studies>.Assessing their potential for further study in computational pharmacological analysis.Why else do people do structure searches?Īs suggested in exercise 1, researchers may be interested in identifying similar structures to learn more about these structurally-related chemicals or they may want create a dataset to serve as a combinatorial library of chemical structural analogs. Click the pull-down menu next to :Hydrogens" and select "Add special" and then click the "Hydrogens" button to add the hydroxyl's "H".Click the "O" in the modified periodic table in the middle of the button panel, and click at the bottom of that new double bond to replace the carbon with a "O".Click the double bond in the 2nd row down and two buttons over to select and click on the middle of the downward pointing bond to convert it to a double bond.Click the button in the 4th row down and three buttons over to select it (it'll turn orange) and then click the "O" to add the group.To create an acetyl group where the "O" atom is attached to the benzene ring: Replace the phenol with a carboxyl manually.Click Similar Structures Search and Edit Structure to make changes to the chemical sketch.Type "salicylic acid" into the input and click on the Best Match result.Start your search on the PubChem Homepage.Searching with PubChem Sketcher- Salicylic acid Example So if you search with a structure, you may be able to find a single PubChem Compound record with everything we know about it which, again, can be quite a lot. PubChem Compound records are created and the information aggregated and added based on standardized chemical structures. Click the "Search For The Structure" button.Manually draw a structure of interest or inputting SMILES, SMARTS, InChI, and InChiKey information.You can search by structure from the start by clicking on Draw Structure (bottom left icon) To use PubChem Sketcher for this purpose: ![]() PubChem Sketcher (similar to other chemical drawing tools, such as ChemDraw and ChemSketch) enables you to create a 2D structure to search those PubChem Compound structures and find their record pages. PubChem has a way for you to manually draw a structure and use it to search for identical or similar structures. A Forensic Chemist has identified the structure of a novel compound found in a poisoning victim by a Medical Examiner and needs to know what it is.An Organic Chemistry research student's experiment has gone awry, but he's identified the chemical structure and would like to know what he's made.A Medicinal Chemist has sketched out what she thinks might be an interesting analog of a known drug and wants to see if she can find a vendor to purchase it.An Analytical Chemist would like to identify a chemical isolated from a bioactive isolate.What if you don't know the name of a chemical, but have a structure and you would like to identify it or learn more about it? Being able to search with that structure can be very helpful, for example: Exercise 2: Searching with PubChem Sketcher ![]()
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