Structure Search
To get to the structure search page select Search | Structure search on the main menu. Then you can conduct your compound query by any of the following methods:
- Structure search via the structure input box
- Additional options
- Functional groups
- Exclusions
The resulting query will generate only those compounds in the Search Results that completely fit the searching options.
Structure search
Structure searches can be done using either one of these two methods: Marvin applet or Chime plugin.
Marvin Applet: This applet uses the browser's built in JavaScript to conduct searches. It is the recommended method of searching on Hit2Lead. To draw a structure, simply click the structure input box. This will pop open a new window called MarvinSketch. Here you will have access to all the industry-standard structure drawing tools. Once the structure is drawn, simply close the MarvinSketch window, and the structure will be automatically transferred to the structure input box on the search page. Then you can set any special filters below the structure input box, and once you click the blue Search button at the bottom, the search will commence.
Chime Plugin: To use this method, you will need both ISIS/DrawTM and Chime installed on your computer. These are two separate programs created by Symyx Technologies (http://www.symyx.com/downloads/index.jsp). ISIS/Draw is used to draw the structures, and Chime allows them to be viewed in your internet browser. Please note that Chime is not compatible with many browsers (including Internet Explorer 7.0 and most Macintosh browsers), so if you're having problems seeing structures, please switch to the Marvin Applet method of searching. To go to the ISIS/Draw structure editor, double-click on the structure input box. Once you have drawn your query in ISIS/Draw, click the Transfer Mode icon in the upper left corner of the drawing area to transfer the drawn structure to the structure input box.
You can perform three different searches by making the appropriate selection in the Search Parameters right below the structure input box:
- Substructure Search. This search enables you to find molecules that have your complete substructure query embedded. Similarity Search. This search method uses Similarity metrics, which measure how similar one molecule is to another, are independent of whether either molecule is a substructure of the other, and are based on Tanimoto coefficients. For effective searching, the minimum similarity value you should use is 40%.
- Exact Structure. This search option allows you to find exact matches to a structure that you have drawn.
Additional Options
You can refine your search by setting some limits that are defined by the Additional Option choices.
- Molecular weight range. Only the most abundant isotope of each element will be considered.
- LogP range. Enter the partition coefficient (lipophilicity) range of the desired chemical structure as an additional molecular parameter. Log(P) is calculated using DayLighTM software version 4.62.
- Rotatable bonds range. Rotational degrees of freedom, as entropic penalties, can be specified for a chosen structure by entering a range or single limitation of rotatable bonds.
- Amount at least value. This defines the minimum physical amount of compound (in mg) that you are willing to acquire or utilize.
- Price less than value. This option allows you to delimit your search parameters by the cost of compounds, which may be valuable for economic/budgetary reasons.
Functional groups
This option is utilized when searching for building blocks only. Various functional groups can be entered: mono-functional, bi-functional or multi-functional.
Building block compounds are also classified by functional groups. There are only those compounds in the search results, which belong to any one of marked groups.
Exclusions
Some compound groups/classes can be excluded from the Search Results by selecting the appropriate boxes in Exclude compounds with section of this additional search refinement tool.
Recent Structures
Your query will be saved in the Recent Structures section in chronological order to the right of the structure input box. To copy one of your recent structures back to the structure input box, simply click on the structure, and it will appear in the box.