Schrödinger Nodes for Suite2018-1 version 0.0.1.7B27VcMf4_L7A58S5A8G55JS by Schrödinger
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.
To use this node in KNIME, install Schrödinger Nodes for Suite2018-1 from the following update site:
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.