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.pre-commit-config.yaml

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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.4.0
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rev: v5.0.0
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hooks:
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# list of supported hooks: https://pre-commit.com/hooks.html
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- id: trailing-whitespace
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# python code formatting
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- repo: https://github.com/psf/black
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rev: 23.1.0
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rev: 24.10.0
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hooks:
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- id: black
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args: [--line-length, "99"]
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# python import sorting
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- repo: https://github.com/PyCQA/isort
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rev: 5.12.0
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rev: 5.13.2
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hooks:
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- id: isort
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args: ["--profile", "black", "--filter-files"]
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# python upgrading syntax to newer version
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- repo: https://github.com/asottile/pyupgrade
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rev: v3.3.1
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rev: v3.19.1
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hooks:
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- id: pyupgrade
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args: [--py38-plus]
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# python docstring formatting
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- repo: https://github.com/myint/docformatter
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rev: v1.7.4
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rev: v1.7.5
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hooks:
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- id: docformatter
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args:
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# python docstring coverage checking
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- repo: https://github.com/econchick/interrogate
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rev: 1.5.0 # or master if you're bold
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rev: 1.7.0 # or master if you're bold
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hooks:
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- id: interrogate
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args:
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# python check (PEP8), programming errors and code complexity
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- repo: https://github.com/PyCQA/flake8
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rev: 6.0.0
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rev: 7.1.1
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hooks:
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- id: flake8
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args:
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# python security linter
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- repo: https://github.com/PyCQA/bandit
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rev: "1.7.5"
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rev: "1.8.2"
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hooks:
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- id: bandit
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args: ["-s", "B101"]
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# yaml formatting
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- repo: https://github.com/pre-commit/mirrors-prettier
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rev: v3.0.0-alpha.6
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rev: v4.0.0-alpha.8
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hooks:
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- id: prettier
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types: [yaml]
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exclude: "environment.yaml"
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# shell scripts linter
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- repo: https://github.com/shellcheck-py/shellcheck-py
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rev: v0.9.0.2
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rev: v0.10.0.1
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hooks:
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- id: shellcheck
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# md formatting
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- repo: https://github.com/executablebooks/mdformat
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rev: 0.7.16
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rev: 0.7.21
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hooks:
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- id: mdformat
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args: ["--number"]
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# word spelling linter
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- repo: https://github.com/codespell-project/codespell
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rev: v2.2.4
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rev: v2.3.0
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hooks:
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- id: codespell
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args:
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# jupyter notebook cell output clearing
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- repo: https://github.com/kynan/nbstripout
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rev: 0.6.1
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rev: 0.8.1
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hooks:
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- id: nbstripout
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# jupyter notebook linting
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- repo: https://github.com/nbQA-dev/nbQA
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rev: 1.6.3
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rev: 1.9.1
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hooks:
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- id: nbqa-black
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args: ["--line-length=99"]

README.md

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<!-- [![Conference](http://img.shields.io/badge/AnyConference-year-4b44ce.svg)](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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```
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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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```
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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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```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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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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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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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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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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wget https://zenodo.org/records/14660031/files/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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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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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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```

citation.bib

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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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}
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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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