Maestro commands - highlight residues
HIghlight and label residues selected on a list. [Requires: Maestro]
Ligand alignment MD refinement 1
A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime […]
Tautomer prediction
Generate the lowest energy tautomers or conformers (or both) for a set of structures, with optional protonation or deprotonation. It ensures that the […]
Docking 1-2
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 […]
Split multimers 1-2
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
Grid generation 1-3
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Shape screening 1-4
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 […]
Build antibody 1
Several antibody models are built using Bioluminate starting from the heavy and light chain sequences. Sequences can be read from an XLS spreadsheet. […]
Database analysis 1-2
Assess the coverage of a database from the distribution of the distance to the nearest neighbor of each molecule in the database. List the three most […]
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 […]