ML Anthology

PLINDER: The Protein-Ligand Interactions Dataset and Evaluation Resource

Janani Durairaj, Yusuf Adeshina, Zhonglin Cao, Xuejin Zhang, Vladas Oleinikovas, Thomas Duignan, Zachary McClure, Xavier Robin, Emanuele Rossi, Guoqing Zhou, Srimukh Prasad Veccham, Clemens Isert, Yuxing Peng, Prabindh Sundareson, Mehmet Akdel, Gabriele Corso, Hannes Stark, Zachary Wayne Carpenter, Michael M. Bronstein, Emine Kucukbenli, Torsten Schwede, Luca Naef
ICMLW 2024
/icmlw/2024/durairaj2024icmlw-plinder/

Abstract

Protein-ligand interactions (PLI) are foundational to small molecule drug design. With computational methods striving towards experimental accuracy, there is a critical demand for a well-curated and diverse PLI dataset. Existing datasets are often limited in size and diversity, and commonly used evaluation sets suffer from training information leakage, hindering the realistic assessment of method generalization capabilities. To address these shortcomings, we present PLINDER, the largest and most annotated dataset to date, comprising 449,383 PLI systems, each with over 500 annotations, similarity metrics at protein, pocket, interaction and ligand levels, and paired unbound (apo) and predicted structures. We propose an approach to generate training and evaluation splits that minimizes task-specific leakage and maximizes test set quality, and compare the resulting performance of DiffDock when re-trained with different kinds of splits.

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Cite

Text

Durairaj et al. "PLINDER: The Protein-Ligand Interactions Dataset and Evaluation Resource." ICML 2024 Workshops: ML4LMS, 2024.

Markdown

[Durairaj et al. "PLINDER: The Protein-Ligand Interactions Dataset and Evaluation Resource." ICML 2024 Workshops: ML4LMS, 2024.](https://mlanthology.org/icmlw/2024/durairaj2024icmlw-plinder/)

BibTeX

@inproceedings{durairaj2024icmlw-plinder,
  title     = {{PLINDER: The Protein-Ligand Interactions Dataset and Evaluation Resource}},
  author    = {Durairaj, Janani and Adeshina, Yusuf and Cao, Zhonglin and Zhang, Xuejin and Oleinikovas, Vladas and Duignan, Thomas and McClure, Zachary and Robin, Xavier and Rossi, Emanuele and Zhou, Guoqing and Veccham, Srimukh Prasad and Isert, Clemens and Peng, Yuxing and Sundareson, Prabindh and Akdel, Mehmet and Corso, Gabriele and Stark, Hannes and Carpenter, Zachary Wayne and Bronstein, Michael M. and Kucukbenli, Emine and Schwede, Torsten and Naef, Luca},
  booktitle = {ICML 2024 Workshops: ML4LMS},
  year      = {2024},
  url       = {https://mlanthology.org/icmlw/2024/durairaj2024icmlw-plinder/}
}