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

By Melissa F. Adasme, Katja L Linnemann, S. Bolz, Florian Kaiser, Sebastian Salentin, V. Haupt, M. Schroeder. Nucleic Acids Res., 2021

1,705 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fa13632c756a92f0f5fc47f337de3890133482d7

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Citations in the corpus

• Structural model of PORCN illuminates disease-associated variants and drug binding sites (2021, background): “A close-up view of ETC-159 docking as determined by Protein-Ligand Interaction Profiler (PLIP) (Adasme et al., 2021) predicts hydrophobic interactions with PORCN Leu405 and Val350 as well as the Val302 and the disease-associated residue Tyr334.”
• The use of a graph database is a complementary approach to a classical similarity search for identifying commercially available fragment merges (2022, background): “PLIP calculates ve types of interaction: hydrophobic contacts, π-stacking interactions (face-to-face or edge-to-face), hydrogen bonds (with the protein as a donor or acceptor), salt bridges (with the protein positively or negatively charged and with metal ions) and halogen bonds [56].”