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05. Searching Online Databases, 5.1 PubChem

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Chris Swain edited this page Apr 27, 2021 · 1 revision

5. Searching Online Databases

5.1 PubChem

PubChem is one of the most straightforward databases to use and it is very popular among college students as its framework is very user-friendly. For this project, the “Draw Search Section” will be used for most of the situations. Occasionally, “Upload ID list” may help once you have got a huge list of known structures to check.

1. To quickly examine your compounds (chem/phys-property, novelty, literature related etc.), the “Draw Structure” section can be useful as it is just like the functionality of what you have learned from SciFinder, Reaxys, or whatever other databases.

You can either type in the SMILES format of your compound or draw the whole structure out within this interface. There are several other options to input your compounds (shown below).

2. After clicking on the “Search for This Structure” button, you will see the following interface (shown below) with multiple functionalities available to optimise your searching results. The searching bar on the top shows the SMILES format of your compound (useful if you have no idea of the SMILES form of your compounds). Also, the “Sort By” utility allows you to specify your needs while searching (multiple properties of compounds are listed).

3. There is a “summary” button down below the first result, as you can see, which can link you to another page with a full list of information about the compound (investigate them on your righthand side).

4. Back to step 2, click on the “Similarity Structures Search” button and you will get a collection of structures which have different degrees of similarity towards the original one. Several options to further segregate those results have been provided on the top bar: Identity, Similarity, Substructure, Superstructure, and 3D Similarity.

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