Cocrystallized 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 […]
MD simulation 1-3
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]
Shape screening 1-3
Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the […]
MCSS 1-2
Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list the compounds that aren't included in this […]
Related PDB structures
Related PDB structures PDB structures containing ligands similar to each LiveReport structures are listed. The PDB structure with the most similar ligand […]
Induced-fit docking 1
Run the default Induced Fit Docking protocol or customize the individual stages. The visual representation of the protein-ligand complexes (molecular […]
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 […]
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 […]