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PubChem Standardization Service Help

This document describes how to use the PubChem standardization web service, which can be found at the URL:

Standardization, in PubChem terminology, is the processing of chemical structures in the same way used to create the PubChem compound database from depositors' original structures. This service will let you see how PubChem would handle any structure you would like to input. (This functionality is also available though PubChem's PUG service.)

Note that this does not include the computation of all the properties normally associated with a PubChem compound, as many of these are computationally expensive. For more thorough processing of your structure data, please see PubChem's deposition system. Further information on the standardization process is available on the main PubChem help page.

Standardization through this service is limited to a single structure at a time, though any number of requests may be submitted. Requests are processed in the order received. All requests are kept private; without your unique 64-bit key, nobody else can see what structures you have submitted.

Steps to standardizing:

1) Select an input format:

SMILES: A simple string in standard SMILES syntax.

InChI: An InChI string.

SDF: Upload an SDF file from your computer.

2) Select an output format:

SMILES: A simple string in standard SMILES syntax.

InChI: An InChI string .

SDF: Returns an SDF format chemical structure, which will contain both SMILES and InChI tags, and a tag with the PubChem CID if this is a structure present in PubChem.

3) Initiate the request:

Submit Job : Begin processing this structure. You will be taken to a self-refreshing waiting page while your request is queued on NCBI's servers. When done, the output will appear as plain text in the desired format.

Save Job : Save the XML specification of this request, mainly for use with PubChem's PUG service.

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