Tools for protein and ligand analysis
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- Plop: minimize ligand and receptor.
- omega.parm: change settings for ligand conformation generation in Omega
- screen3d: align ligands in 3D. Useful to see if bioactive conformation is sampled.
- Phenix: calculate electron densities and display them in Pymol
- filter.py: calculate atoms distances of DOCK poses
- FlexPepDock: peptide docking
- DOCK Sampling: pose sampling in DOCK
- DOCK6 RMSD: calculate ligand RMSDs