Docking 1-3
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 […]
Clustering 1-3
Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]
Docking 1
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 […]
Compare confo search methods
Run a conformational search with various methods and compare the lowest energy conformers. Parse the log file to extract relevant information. [Requires: […]
Bioisosteres
Bioisosteres - in LiveDesign Replace functional groups of each LiveReport ligand with bioisosteres, generating all the single replacements. The […]
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 […]
Database preparation 1-2
Label compounds from a single vendor. Prepare and filter compounds by various criteria. Based on: Clark, D.E.; Higgs, C.; Wren, S.P.; Dyke, H.J.; Wong, M.; […]
MM Conformational search 1-4
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
Sequence converter
Metanode to run the Sequence converter utility.