The antibody structure can be split into Fc, Fab and Fv domains. The node scans proteins for residues that are candidates for mutation and evaluate the […]
Reactive protein residues are listed and compared for a set of structures. They are also highlighted when inspecting the structures. [Requires: […]
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Illustrate the Output column structure options (output only, input plus output, and output replaces input). The workflow also demonstrates a potential […]
The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between […]
Maximum Common Substructure Search (MCS): Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list […]
Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, […]
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
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 […]
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.