Validate parameters 1-2
Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an […]
Shape screening 1-3
Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the […]
Clustering 1-4
Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]
GroupBy 1-2
Illustrate how to use the GroupBy node in the context of the ionization form prediction over a range of pH. Various aggregation methods are used: […]
QM Conformational search 1-2
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
Binding site 1-2
Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: SiteMap] The SiteMap […]
Node Conformer cluster
[Version: 2.9.0] [Requires: Maestro, (ConfGen)]
Unique molecule titles
Ensure unique molecule titles (using the KNIME RowID or the Schrödinger dedicated node). This is useful in the context of Canvas. [Requires: Maestro, Canvas]
FEP analysis 2
An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including […]
KNIME-Maestro connector
Uses the KNIME-Maestro connector (replacing the Run Maestro 1:1 metanode) to alter some structures in the middle of a workflow, pick residues to sample in a […]