Software | Complexes | Input format | MD | Configurable | Extensible | Web | CLI | Ref. |
---|
ProLIF | All | MDAnalysis and RDKitc | ✓ | ✓ | ✓ | | | |
IChem | LP | MOL2 | | ✓ | | | ✓ | [4] |
PLIP | Alla | PDB | | ✓ | | ✓ | ✓ | [15, 18] |
Arpeggio | Alla | PDB | | ✓ | | ✓ | ✓ | [16] |
PyPLIF HIPPOS | LPa | PDBQT, MOL2 | | ✓ | | | ✓ | [17] |
getContacts | Alla,b | VMDc | | ✓ | | | ✓ | [19] |
MD-IFP | LPa | MDAnalysisc | ✓ | | | | | [10] |
ODDT | LP | OpenBabel and RDKitc | | ✓ | | | | [20] |
- MD native support of MD trajectories; Web available through a webserver; CLI command-line interface; LP Ligand–Protein; All all combinations between ligand, protein, DNA, and RNA molecules
- aRelies on residue and atom naming convention to assign charges and/or aromaticity
- bOnly supports hydrogen-bond, hydrophobic and van der Waals contacts for LP complexes
- cCompatible with the input formats supported by the aforementioned libraries