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. 2021 Jul 2;49(W1):W530-W534.
doi: 10.1093/nar/gkab294.

PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA

Melissa F Adasme  1 , Katja L Linnemann  1 , Sarah Naomi Bolz  1 , Florian Kaiser  2 , Sebastian Salentin  1 , V Joachim Haupt  2 , Michael Schroeder  1
Affiliations

PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA

Melissa F Adasme et al. Nucleic Acids Res. .

Abstract

With the growth of protein structure data, the analysis of molecular interactions between ligands and their target molecules is gaining importance. PLIP, the protein-ligand interaction profiler, detects and visualises these interactions and provides data in formats suitable for further processing. PLIP has proven very successful in applications ranging from the characterisation of docking experiments to the assessment of novel ligand-protein complexes. Besides ligand-protein interactions, interactions with DNA and RNA play a vital role in many applications, such as drugs targeting DNA or RNA-binding proteins. To date, over 7% of all 3D structures in the Protein Data Bank include DNA or RNA. Therefore, we extended PLIP to encompass these important molecules. We demonstrate the power of this extension with examples of a cancer drug binding to a DNA target, and an RNA-protein complex central to a neurological disease. PLIP is available online at https://plip-tool.biotec.tu-dresden.de and as open source code. So far, the engine has served over a million queries and the source code has been downloaded several thousand times.

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Figures

Graphical Abstract
Graphical Abstract
The Protein-Ligand Interaction Profiler. PLIP detects molecular interactions in 3D structures including DNA and RNA.
Figure 1.
Figure 1.
PLIP web tool result page. On the left is a menu for ligands and binding sites, in the middle an image of a selected binding site and on the right a table with details of the interactions.
Figure 2.
Figure 2.
Nucleic acid structures growth in PDB. Number of nucleic acid structures released annually since 2000 and the total aggregated structures.
Figure 3.
Figure 3.
Examples. (A) FUS binding the UGGUG (PDB ID: 6G99), (B) XR5944 binding the TFF1 estrogen response element (PDB ID: 2MG8) and (C) GTP binds RNA polymerase II and DNA/RNA of the elongation complex (PDB ID: 2E2H). Ligands are shown in orange and receptors in blue, green or purple gray. Protein residues are labeled in black and DNA/RNA bases in red.
See this image and copyright information in PMC

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