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PocketVina Atlas

Cite

If you use PocketVina Atlas, please cite the PocketVina paper, and the tools it builds on.

PocketVina

Sarigun A, Uyar B, Franke V, Akalin A. PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning. arXiv:2506.20043 (2025).

@misc{sarigun2025pocketvinaenablesscalablehighly,
      title={PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning}, 
      author={Ahmet Sarigun and Bora Uyar and Vedran Franke and Altuna Akalin},
      year={2025},
      eprint={2506.20043},
      archivePrefix={arXiv},
      primaryClass={q-bio.QM},
      url={https://arxiv.org/abs/2506.20043}, 
}

Paper on arXivPocketVina on GitHub

Please also cite

The tools PocketVina runs: P2Rank finds the pockets, the Vina family docks the compounds.

P2Rank

P2Rank
@article{krivak2018p2rank,
  title   = {P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure},
  author  = {Krivák, Radoslav and Hoksza, David},
  journal = {Journal of cheminformatics},
  volume  = {10},
  pages   = {1--12},
  year    = {2018},
  publisher = {Springer}
}

Vina family

Vina-GPU 2.1
@article{tang2024vina,
  title   = {Vina-GPU 2.1: towards further optimizing docking speed and precision of AutoDock Vina and its derivatives},
  author  = {Tang, Shidi and Ding, Ji and Zhu, Xiangyu and Wang, Zheng and Zhao, Haitao and Wu, Jiansheng},
  journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year    = {2024},
  publisher = {IEEE}
}
Vina-GPU 2.0
@article{ding2023vina,
  title   = {Vina-GPU 2.0: further accelerating AutoDock Vina and its derivatives with graphics processing units},
  author  = {Ding, Ji and Tang, Shidi and Mei, Zheming and Wang, Lingyue and Huang, Qinqin and Hu, Haifeng and Ling, Ming and Wu, Jiansheng},
  journal = {Journal of chemical information and modeling},
  volume  = {63},
  number  = {7},
  pages   = {1982--1998},
  year    = {2023},
  publisher = {ACS Publications}
}
Accelerating AutoDock Vina with GPUs
@article{tang2022accelerating,
  title   = {Accelerating autodock vina with gpus},
  author  = {Tang, Shidi and Chen, Ruiqi and Lin, Mengru and Lin, Qingde and Zhu, Yanxiang and Ding, Ji and Hu, Haifeng and Ling, Ming and Wu, Jiansheng},
  journal = {Molecules},
  volume  = {27},
  number  = {9},
  pages   = {3041},
  year    = {2022},
  publisher = {MDPI}
}
AutoDock Vina
@article{trott2010autodock,
  title   = {AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading},
  author  = {Trott, Oleg and Olson, Arthur J},
  journal = {Journal of computational chemistry},
  volume  = {31},
  number  = {2},
  pages   = {455--461},
  year    = {2010},
  publisher = {Wiley Online Library}
}

PocketVina Atlas

To refer to the atlas itself, name the release and the address:

PocketVina Atlas, Release v1.1. https://bimsbstatic.mdc-berlin.de/akalin/asarigun/pocketvina_atlas/
Docked with PocketVina 0.1.0; desalted forms of salt entries: PocketVina 0.2.0 against the AlphaFold human proteome.

A resource of the Bioinformatics and Omics Data Science Platform (Akalin Lab), Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center, Berlin.

Data and tools the atlas uses