Split multimers 1
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
Protein model building
Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and the binding site is […]
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 […]
Similarity 1-2
Find the most similar compounds to a sketched molecule in a database. Screen the same database against several query structures. [Requires: Canvas]
Ligand alignment MD refinement 2
A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime […]
Jaguar pKa
Evaluate the pKa of specified atoms using Jaguar. [Requires: Ligprep, Jaguar] [Keywords: Quantum mechanics, pKa, parameter flow variables]
Watermap 1
A Watermap job is submitted and the map inspected in Maestro. It could be run on several complexes in one run.
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 […]
Parameter flow variables 1
Use the parameter flow variables to control command-line options not exposed in the configuration panel. This is illustrated for the protein preparation, […]
Epik
Predict ligand states with Epik and report the ionization form matrix. Generate with LigPrep minimized ionization-tautomeric forms ready to be […]