Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints

By G. Marcou, Didier Rognan. Journal of Chemical Information and Modeling, 2007

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KLIFS: a structural kinase-ligand interaction database (2015, positive): “front cleft, gate area and/or back cleft (type I, I (1)2 , II and III (8)) to allow for the systematic analysis of kinase-ligand interaction fingerprints (IFPs) (9) with different residues in the kinase binding site (Figure 2A) (5) in order to identify kinase (family) specific interaction features a”
Molecular docking and ligand specificity in fragment-based inhibitor discovery (2009, background): “This reflects two concerns in the community: first, fragments may be more promiscuous in their binding modes than larger 'drug-like' molecules, and this is difficult to predict; second, docking scoring functions are inaccurate even for the larger molecules against which they have often been paramete”
PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA (2021, background): “…suffer from some limitations: (29–33) detect only a limited set of interaction types and do not offer 3D visualisation, (34) requires extensive preparation of input files, (38) is only commercially available and (35,36) are limited to binary interaction fingerprints and do not cover DNA and RNA.”
Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures (2017, methodology): “FingerPrintLib [15] and PyPLIF [16] calculatemultiple interaction types but are restricted to protein interactions with small organic molecule ligands only.”