IconProtein Alignment 

Extract one monomer from each of the two multimers. Align the binding sites (via the 'Align Binding Sites' node) or the whole structure (using the 'Protein […]

IconOutput column structure 

Illustrate the Output column structure options (output only, input plus output, and output replaces input). The workflow also demonstrates a potential […]

IconCocrystallized ligand redocking 2 

Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized […]

IconDatabase preparation 1 

Label compounds from a single vendor. Prepare and filter compounds by various criteria. Based on: Clark, D.E.; Higgs, C.; Wren, S.P.; Dyke, H.J.; Wong, M.; […]

IconDatabase preparation 1-3 

Label compounds from a single vendor. Prepare and filter compounds by various criteria. Based on: Clark, D.E.; Higgs, C.; Wren, S.P.; Dyke, H.J.; Wong, M.; […]

IconBioisoster replacement 

Functional groups are replaced with bioisosteres that are available in the literature. [Requires: Maestro]

IconTools 

Extract the atom-level properties to list the PDB conversion problems. [Requires: -] See other workflow examples using the Extract atom/bond […]

IconDocking 1-3 

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 […]