Cocrystallized ligand redocking 1
Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized […]
Readers and Writers
Read and write structure files. Read a list of PDB files from a directory. [Requires: Maestro] See also: - Docking - Grid generation: Glide grid […]
Sitemap and docking
Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock […]
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 […]
Docking 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 […]
Bioluminate 1-4
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 […]
Grid generation 1
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
MD simulation 1
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]
KNIME Server - QikProp
Workflow to be run on a KNIME server and invoked from a LiveDesign Computational model. [Requires: LigPrep, QikProp]
Run PyMOL 1
[Version: 6.8 Requires: Maestro, PyMOL Keywords: PyMOL, visualization]