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<!-- [](https://papers.nips.cc/paper/2020) -->
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- [ ![ Data DOI] ( https://zenodo.org/badge/DOI/10.5281/zenodo.14478459 .svg )] ( https://doi.org/10.5281/zenodo.14478459 )
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+ [ ![ Data DOI] ( https://zenodo.org/badge/DOI/10.5281/zenodo.14660031 .svg )] ( https://doi.org/10.5281/zenodo.14660031 )
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<img src =" ./img/FlowDock.png " width =" 600 " >
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``` bash
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# pretrained FlowDock weights
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- wget https://zenodo.org/records/14478459 /files/flowdock_checkpoints.tar.gz
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+ wget https://zenodo.org/records/14660031 /files/flowdock_checkpoints.tar.gz
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tar -xzf flowdock_checkpoints.tar.gz
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rm flowdock_checkpoints.tar.gz
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```
@@ -99,19 +99,19 @@ tar -xzf flowdock_data_cache.tar.gz
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rm flowdock_data_cache.tar.gz
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# cached data for PDBBind, Binding MOAD, DockGen, and the PDB-based van der Mers (vdM) dataset
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- wget https://zenodo.org/records/14478459 /files/flowdock_pdbbind_data.tar.gz
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+ wget https://zenodo.org/records/14660031 /files/flowdock_pdbbind_data.tar.gz
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tar -xzf flowdock_pdbbind_data.tar.gz
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rm flowdock_pdbbind_data.tar.gz
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- wget https://zenodo.org/records/14478459 /files/flowdock_moad_data.tar.gz
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+ wget https://zenodo.org/records/14660031 /files/flowdock_moad_data.tar.gz
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tar -xzf flowdock_moad_data.tar.gz
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rm flowdock_moad_data.tar.gz
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- wget https://zenodo.org/records/14478459 /files/flowdock_dockgen_data.tar.gz
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+ wget https://zenodo.org/records/14660031 /files/flowdock_dockgen_data.tar.gz
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tar -xzf flowdock_dockgen_data.tar.gz
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rm flowdock_dockgen_data.tar.gz
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- wget https://zenodo.org/records/14478459 /files/flowdock_pdbsidechain_data.tar.gz
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+ wget https://zenodo.org/records/14660031 /files/flowdock_pdbsidechain_data.tar.gz
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tar -xzf flowdock_pdbsidechain_data.tar.gz
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rm flowdock_pdbsidechain_data.tar.gz
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```
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<details >
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** NOTE:** The following steps (besides downloading PDBBind and Binding MOAD's PDB files) are only necessary if one wants to fully process each of the following datasets manually.
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- Otherwise, preprocessed versions of each dataset can be found on [ Zenodo] ( https://zenodo.org/records/14478459 ) .
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+ Otherwise, preprocessed versions of each dataset can be found on [ Zenodo] ( https://zenodo.org/records/14660031 ) .
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Download data
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@@ -283,29 +283,49 @@ Download baseline method predictions and results
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``` bash
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# cached predictions and evaluation metrics for reproducing structure prediction paper results
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- wget https://zenodo.org/records/14478459/files/chai_baseline_method_predictions.tar.gz
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+ wget https://zenodo.org/records/14660031/files/alphafold3_baseline_method_predictions.tar.gz
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+ tar -xzf alphafold3_baseline_method_predictions.tar.gz
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+ rm alphafold3_baseline_method_predictions.tar.gz
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+
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+ wget https://zenodo.org/records/14660031/files/chai_baseline_method_predictions.tar.gz
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tar -xzf chai_baseline_method_predictions.tar.gz
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rm chai_baseline_method_predictions.tar.gz
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- wget https://zenodo.org/records/14478459 /files/diffdock_baseline_method_predictions.tar.gz
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+ wget https://zenodo.org/records/14660031 /files/diffdock_baseline_method_predictions.tar.gz
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tar -xzf diffdock_baseline_method_predictions.tar.gz
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rm diffdock_baseline_method_predictions.tar.gz
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- wget https://zenodo.org/records/14478459 /files/dynamicbind_baseline_method_predictions.tar.gz
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+ wget https://zenodo.org/records/14660031 /files/dynamicbind_baseline_method_predictions.tar.gz
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tar -xzf dynamicbind_baseline_method_predictions.tar.gz
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rm dynamicbind_baseline_method_predictions.tar.gz
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- wget https://zenodo.org/records/14478459 /files/flowdock_baseline_method_predictions.tar.gz
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+ wget https://zenodo.org/records/14660031 /files/flowdock_baseline_method_predictions.tar.gz
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tar -xzf flowdock_baseline_method_predictions.tar.gz
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rm flowdock_baseline_method_predictions.tar.gz
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- wget https://zenodo.org/records/14478459/files/flowdock_hp_baseline_method_predictions.tar.gz
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+ wget https://zenodo.org/records/14660031/files/flowdock_aft_baseline_method_predictions.tar.gz
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+ tar -xzf flowdock_aft_baseline_method_predictions.tar.gz
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+ rm flowdock_aft_baseline_method_predictions.tar.gz
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+
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+ wget https://zenodo.org/records/14660031/files/flowdock_esmfold_baseline_method_predictions.tar.gz
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+ tar -xzf flowdock_esmfold_baseline_method_predictions.tar.gz
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+ rm flowdock_esmfold_baseline_method_predictions.tar.gz
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+
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+ wget https://zenodo.org/records/14660031/files/flowdock_hp_baseline_method_predictions.tar.gz
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tar -xzf flowdock_hp_baseline_method_predictions.tar.gz
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rm flowdock_hp_baseline_method_predictions.tar.gz
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- wget https://zenodo.org/records/14478459 /files/neuralplexer_baseline_method_predictions.tar.gz
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+ wget https://zenodo.org/records/14660031 /files/neuralplexer_baseline_method_predictions.tar.gz
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tar -xzf neuralplexer_baseline_method_predictions.tar.gz
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rm neuralplexer_baseline_method_predictions.tar.gz
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+
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+ wget https://zenodo.org/records/14660031/files/vina_p2rank_baseline_method_predictions.tar.gz
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+ tar -xzf vina_p2rank_baseline_method_predictions.tar.gz
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+ rm vina_p2rank_baseline_method_predictions.tar.gz
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+
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+ wget https://zenodo.org/records/14660031/files/rfaa_baseline_method_predictions.tar.gz
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+ tar -xzf rfaa_baseline_method_predictions.tar.gz
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+ rm rfaa_baseline_method_predictions.tar.gz
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```
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Reproduce paper result figures
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``` bibtex
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@article{morehead2024flowdock,
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- title={FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction},
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- author={Alex Morehead and Jianlin Cheng},
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- year={2024},
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- eprint={2412.10966},
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- archivePrefix={arXiv},
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- primaryClass={cs.LG},
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- url={https://arxiv.org/abs/2412.10966},
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+ title={FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction},
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+ author={Morehead, Alex and Cheng, Jianlin},
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+ journal={arXiv preprint arXiv:2412.10966},
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+ year={2024}
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}
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```
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