MM Conformational search 1-3
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
Sequence converter
Metanode to run the Sequence converter utility.
MCSS 1-4
Maximum Common Substructure Search (MCS): Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list […]
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 […]
Bioluminate 1
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 […]
Docking 1
Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a […]
Split multimers 1-2
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
QM Conformational search 1
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
Docking 1-2
Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a […]
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 […]