Calculate molecular orbitals and vibrational frequencies. [Requires: Ligprep, Jaguar] [Keywords: quantum mechanics, semi-empirical, parameter flow […]
Generate QSAR models for a chosen property of a set of compounds, and apply the QSAR nodel to other compounds, with either traditional QSAR methods or […]
Run the default Induced Fit Docking protocol or customize the individual stages. The visual representation of the protein-ligand complexes (molecular […]
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]
Create libraries by substituting one or several attachments on a core structure with fragments from reagent compounds. Unique identifiers are assigned to […]
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: SiteMap] The SiteMap […]
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]
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.