Related PDB structures PDB structures containing ligands similar to each LiveReport structures are listed. The PDB structure with the most similar ligand […]
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
Ensure unique molecule titles (using the KNIME RowID or the Schrödinger dedicated node). This is useful in the context of Canvas. [Requires: Maestro, Canvas]
Maximum Common Substructure Search (MCS): Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list […]
A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime […]
Search a set of structures against a sketched query molecule or SMARTS patterns. Report the compounds that don't pass all the REOS filters. [Requires: […]
[Version: 3.0.0] [Requires: Maestro]
[Version: 2.9.0] [Requires: Epik, LigPrep]
A Watermap job is submitted and the map inspected in Maestro. It could be run on several complexes in one run.
[Version: 7.5 Requires: (Prime) Keyworkds: Maestro commands, scripting]
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 mail@nodepit.com.
Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.