Reagent preparation ensures that the input structures are all-atom, 3D structures, and that they have the appropriate
information stored with them to construct the molecules that are used in screening or are added to the library.
Apart from 2D-to-3D conversion and structure variation and cleanup, which is performed by LigPrep,
the main task in this node is to select a reagent type (a functional group) and to identify the bond
in the functional group that is replaced when the reagent is added to the core.
The reagent preparation job attempts to identify the selected functional group in each structure.
Structures that match are then prepared using LigPrep. The structure source does not therefore need to contain
only structures that have the desired functional group: structures that don't are filtered out.
Duplicates are not filtered out, however, so you should ensure that the input file does not contain duplicates.
The output file contains the prepared reagents. There might be several output structures per input structure if
the molecule can exist in several low-energy forms.
You must run this node for each reagent type that will be used in combinatorial screening or combinatorial library enumeration.
Column containing input
Choose the input column containing the reagents
Functional group to identify
Protonate or deprotonate the reagents to represent the actual form in water in the given pH range.
If deselected, the structure's initial ionization state is retained.
Select this option to generate tautomers of the input structures. Ionized structures might have a different tautomeric form from the unionized structures.
Use Epik for ionization and tautomerization
Select this option to use Epik for ionization and tautomerization rather than the ionizer and the tautomerizer.
Enter the number of stereoisomers to generate. If the input structures are 2D and have chiral centers but do not have chirality information, you should ensure that the number specified covers the possible combinations.
Generate low-energy ring conformations
If the input structures contain rings that can exist in more than one low-energy conformation, enter the number of likely low-energy conformations in this text box. Ring conformations are not searched during docking, so the conformations must be set up beforehand.
Input data table containing molecules in Maestro format
Wait a sec! You want to explore and install nodes even faster? We highly recommend our
NodePit for KNIME
extension for your KNIME Analytics Platform.
Do you have feedback, questions, comments about NodePit, want to support this platform, or want your own nodes or workflows listed here as well?
Do you think, the search results could be improved or something is missing?
Then please get in touch! Alternatively, you can send us an email to email@example.com,
follow @NodePit on Twitter,
or chat on Gitter!
Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.