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.; […]
Bioluminate 1-3
The antibody structure can be split into Fc, Fab and Fv domains. The node scans proteins for residues that are candidates for mutation and evaluate the […]
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 […]
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 […]
MM Conformational search 1-2
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
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: […]
Database analysis 1
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 […]
FEP analysis 2
An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including […]
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 […]