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Melissa F. Adasme, Katja L Linnemann, Sarah Naomi Bolz, Florian Kaiser, Sebastian Salentin, V. Joachim Haupt, Michael Schroeder
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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Adasme, M. F., Linnemann, K. L., Bolz, S. N., Kaiser, F., Salentin, S., Haupt, V. J., & Schroeder, M. (2021). PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA. Nucleic Acids Research, 49(W1), W530–W534. https://doi.org/10.1093/nar/gkab294
Adasme, Melissa F., et al. "PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA." Nucleic Acids Research, vol. 49, no. W1, 2021, pp. W530–W534, https://doi.org/10.1093/nar/gkab294.
Adasme, Melissa F., Katja L Linnemann, Sarah Naomi Bolz, Florian Kaiser, Sebastian Salentin, V. Joachim Haupt, and Michael Schroeder. "PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA." Nucleic Acids Research 49, no. W1 (2021): W530–W534. https://doi.org/10.1093/nar/gkab294.
Adasme M. F., Linnemann K. L., Bolz S. N. [и др.] PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA // Nucleic Acids Research. — 2021. — Vol. 49, № W1. — P. W530–W534. — URL: https://doi.org/10.1093/nar/gkab294
@article{adasme2021plip,
title = {{PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA}},
author = {Melissa F. Adasme and Katja L Linnemann and Sarah Naomi Bolz and Florian Kaiser and Sebastian Salentin and V. Joachim Haupt and Michael Schroeder},
journal = {Nucleic Acids Research},
year = {2021},
volume = {49},
number = {W1},
pages = {W530--W534},
doi = {10.1093/nar/gkab294},
url = {https://doi.org/10.1093/nar/gkab294}
}TY - JOUR AU - Adasme, Melissa F. AU - Linnemann, Katja L AU - Bolz, Sarah Naomi AU - Kaiser, Florian AU - Salentin, Sebastian AU - Haupt, V. Joachim AU - Schroeder, Michael TI - PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA JO - Nucleic Acids Research VL - 49 IS - W1 SP - W530 EP - W534 PY - 2021 DA - 2021/04/13 DO - 10.1093/nar/gkab294 UR - https://doi.org/10.1093/nar/gkab294 ER -
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