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Table 1 Comparative table of features available in non-commercial IFP software

From: ProLIF: a library to encode molecular interactions as fingerprints

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]

  1. 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
  2. aRelies on residue and atom naming convention to assign charges and/or aromaticity
  3. bOnly supports hydrogen-bond, hydrophobic and van der Waals contacts for LP complexes
  4. cCompatible with the input formats supported by the aforementioned libraries