QM Conformational search 1-3
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
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 […]
Split multimers 1-3
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
Library design workshop
Bioisostere and R-group enumeration using custom or predefined isosteres and libraries. Reaction-Based Enumeration to rapidly generate idea molecules with […]
Binding site 1
Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: SiteMap] The SiteMap […]
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 […]
Watermap 2
A Watermap job is submitted and the map inspected in Maestro. It could be run on several complexes in one run.
Binding Pose Metadynamics
Various binding configurations of a single ligand in a single binding site are ranked.
Protonation forms
Protonation forms in LiveDesign Generate protonation forms with Epik and populates the LiveReport with the structure of the most probable form in a new […]
Split multimers 1
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]