Contents: - Structure Search Basics - Substructure Search - Similarity Search - Advanced Search

Introduction

ChemSpider supports the use of chemical structures as search queries. There are lots of different ways that you can input your structure. This page will outline how to perform structure searches to find exact matches, as well as substructure searches and similarity searches. It will also cover how to construct advanced searches, which can combine substructure or similarity searches with other kinds of search.

Basics

The structure search interface, showing the embedded structure editor

Step 1

Select the More Searches menu from the top toolbar and choose Structure Search from the dropdown menu. Click on the structure picture to open the ChemSpider Input Chemical Structure dialog. The Draw Structure tab may be selected(default setting) but this tab may not not be your current default setting.

 

Step 2

There are three ways to enter a chemical structure:
  1. Select the Convert identifier to structure tab. This tab allows you to enter a chemical name and auto-generate a structure by selecting Convert.
    Example showing how you can use the Convert structure option to generate an editable structure from a name . Eg. Morphine

    Example showing how you can use the Convert structure option to generate an editable structure from a name . Eg. Morphine

    Click Accept to accept the structure or Draw Structure to change features of the structure. For example you might want to change the pre-defined stereochemistry of the bonds. On completion of the editing of the structure you can Clean Molecule, Accept or Cancel.
  2. Alternatively, you can draw the structure in your favourite drawing package and save it as a mol, sdf, cdx or skc file to your desktop. You can then upload the file to ChemSpider using the Load button. This is also the way to use any existing structure files you have in a ChemSpider search. There are also options to Load a structure from a JPEG or GIF image, which will run an OCR process and let you correct any errors before accepting the structure.

  3. You can also draw the structure using one of the structure editors available in ChemSpider, we currently provide two HTML 5 editors Ketcher and Elemental and a Java-based editor JDraw, you can select your preferred editors using the tabs. Click on the left pane of the Structure tab to activate and select the tools. structure editor tabs

Step 3

Click on Search and on completion of the search, you should either get to the corresponding record (in certain cases where there is no exact mass, you may see a list of results).  

codiene

 

Substructure Search

Substructure searching will return all results which contain the structure you have entered, including the exact structure you have entered if it is on ChemSpider.

substruct_input

To perform this kind of search, draw, convert or upload your structure (see Structure Search Basics for more information). Then select the “Substructure” radio button, and click “Search”.

substruct results

This type of search can be combined with properties search in order to narrow your results. For more information, check out Advanced Search.

Similarity Search

Similarity searching will return results which are chemically similar to the structure you have entered. Unlike substructure search, it is not limited to compounds which contain the exact substructure you have entered. However, it will return compounds which have many motifs in common. In order to ensure that the results you get are more likely to be relevant, most of the time it is best to limit Similarity Searching to a minimum of 90% similarity.

To perform this kind of search, draw, convert or upload your structure (see Structure Search Basics for more information). Then select the “Similarity” radio button. At this point, you will be able to specify percent similarity and the similarity measure you want to use (Tanimoto, Tversky, or Euclidean). Each option determines similarity slightly differently, so if you don’t get the results you want on one try the others. Then click “Search”.

The above similarity search may be repeated with the Tversky search algorithms and the results should be similar. When the search is repeated with the Euclidean algorithm, a much larger set of structures are returned(> 10,000) as shown in the following screen.

This type of search can be combined with properties search in order to narrow your results. For more information, check out Advanced Search.
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