Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: SiteMap] The SiteMap […]
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 […]
Run a conformational search with various methods and compare the lowest energy conformers. Parse the log file to extract relevant information. [Requires: […]
Generate the lowest energy tautomers or conformers (or both) for a set of structures, with optional protonation or deprotonation. It ensures that the […]
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: […]
Reactive protein residues are listed and compared for a set of structures. They are also highlighted when inspecting the structures. [Requires: […]
Extract the atom-level properties to list the PDB conversion problems. [Requires: -] See other workflow examples using the Extract atom/bond […]
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 […]
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
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.