A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime […]
A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime […]
Dock and covalently binds ligands to the specified reactive residue in the protein target using Michael addition reaction type. [Requires: ProteinPrep, […]
Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, […]
Structures and properties are retrieved from Live Design. New properties are added to an existing Live report. [Products: Live Design]
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]