Generating a Library
Use LIBRARY>>2D>>Create to create a new library. When creating a library for the first time, you will be prompted to specify a location, which by default is a subfolder called MMPScreenLibraries in the ADMET Predictor installation folder.
A subsequent options dialog allows you to provide a name for the library and a file containing the chemical structures to place inside of the library. SD, SMILES and CTK files can be used for the structures. Once the name and file are specified, you need to specify which molecule attributes should be copied from the file to the library. Those attributes will be imported along with matching structures when the library is later queried, as described below.
Note that salts and other small fragments will be stripped when adding each molecule to the library, such that only the largest fragment (by atom count) is retained. For reference, any removed fragments are preserved as an attribute of the library record using SMILES notation.
Searching a Library
ADMET Predictor provides several ways to search libraries. Note that all features described below are available under the LIBRARY>>2D menu.
Search by Structure
Used to retrieve library structures that match a query and then either import those structures into ADMET Predictor or export them to a separate CTK file. Both partial (substructure) matching and exact matching are supported. Queries can be typed manually (encoded format), loaded from a file, pasted from a sketch application such as ChemDraw, or imported directly from MedChem Designer™.
Search by Text
Similar to the structure query feature described above, except that the query must be a text string rather than a substructure. By default, all text attributes stored in the libraries will be searched; partial matching is allowed and case is always ignored. If you know the identifiers within the library and prefer to search by identifiers, the dialog-box provides an option to do so.
Search by Similarity
Used to find library molecules that are structurally similar to a single selected molecule in the Compounds tab, and then either import those structures into ADMET Predictor or export them to a separate CTK file. The measure of structural similarity is based on the same criteria used to generate molecular pairs, as described in the section entitled Pair generation options.
Search by Similarity Using File
Similar to Search by Similarity described above. However, in this case you can use multiple query structures contained in an external file. The results will be exported to a separate CTK file.
Import/Export the Library
Import Compounds
Imports all compounds from one or more libraries directly into ADMET Predictor.
Export Compounds
Exports all compounds from one or more libraries to an external file.