├── resources └── cover.png ├── LICENSE └── README.md /resources/cover.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KyGao/awesome-docking/HEAD/resources/cover.png -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 |

2 | 🧬 Awesome Docking 3 |

4 |
5 | 6 | [![ 7 | Awesome](https://awesome.re/badge.svg)](https://awesome.re) ![Stars](https://img.shields.io/github/stars/KyGao/awesome-docking?color=yellow&labelColor=555555) ![Forks](https://img.shields.io/github/forks/KyGao/awesome-docking?color=blue&label=Fork&labelColor=555555) 8 |
9 |

10 | 11 |

12 | 13 | **AlphaFold-latest**🔥 (with newly updated **AlphaFold3**🔥 )and **RFAA**🔥 have revolutionize the scope of docking. Previous work was focused on modeling different components separately, but these two studies have used a single model to simultaneously model all biomolecular interactions. Here is a curated paper list containing all kinds of deep learning-based docking, covering **Protein-Ligand Docking**, **Protein-Protein Docking**, **Protein-Nucleic Acid Docking**, and **Covalent Docking**. Additionally, we refer to works capable of handling various types of docking scenarios simultaneously as '**Versatile Docking**'. Future work will encompass tools, datasets, scoring function design, and other relvant topics. Within each category, entries are listed in reverse chronological order, with the most recent first. If a paper has multiple versions, we reference the initial publication date. The following badges are used for according purpose: 14 | 15 | ![](https://img.shields.io/badge/paper-5291C8?style=flat&logo=Read.cv&labelColor=555555) ![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555&logocolor=555555) ![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555) ![](https://img.shields.io/badge/tag-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 16 | 17 | If you have a paper or resource you'd like to add, please submit a pull request or open an issue. 18 | 19 | ## Categories 20 | 21 | - [Versatile Docking](#versatile-docking) 22 | - [Protein-Ligand Docking](#protein-ligand-docking) 23 | - [2025 -- Protein-Ligand](#2025----protein-ligand) 24 | - [2024 -- Protein-Ligand](#2024----protein-ligand) 25 | - [2023 -- Protein-Ligand](#2023----protein-ligand) 26 | - [2022 -- Protein-Ligand](#2022----protein-ligand) 27 | - [Protein-Protein Docking](#protein-protein-docking) 28 | - [2024 -- Protein-Protein](#2024----protein-protein) 29 | - [2023 -- Protein-Protein](#2023----protein-protein) 30 | - [2022 -- Protein-Protein](#2022----protein-protein) 31 | - [2021 -- Protein-Protein](#2021----protein-protein) 32 | - [Protein-Nucleic Acid Docking](#protein-nucleic-acid-docking) 33 | - [2023 -- Protein-Nucleic Acid](#2023----protein-nucleic-acid) 34 | - [Covalent Docking](#covalent-docking) 35 | - [Survey](#survey) 36 | - [Protein-Ligand](#protein-ligand) 37 | - [Protein-Protein](#protein-protein) 38 | - [Protein-Nucleic Acid](#protein-nucleic-acid) 39 | - [Covalent](#covalent) 40 | - [Traditional Docking Tools](#traditional-docking-tools) 41 | - [Open-source and free access](#open-source-and-free-access) 42 | - [Commercial tools](#commercial-tool) 43 | 44 | --- 45 | 46 | ## Versatile Docking 47 | 48 | **Boltz-1: DemocratizingBiomolecularInteractionModeling** 49 | Jeremy Wohlwend*, Gabriele Corso*, Saro Passaro*, Mateo Reveiz, Ken Leida, Wojtek Swiderski, Tally Portnoi, Itamar Chinn, Jacob Silterra, Tommi Jaakkola, Regina Barzilay 50 | *Report, Nov 2024* 51 | [![](https://img.shields.io/badge/report-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://gcorso.github.io/assets/boltz1.pdf) 52 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/jwohlwend/boltz) 53 | ![Stars](https://img.shields.io/github/stars/jwohlwend/boltz?color=yellow&style=social) 54 | 55 | **Chai-1 Technical Report** 56 | Chai-1 Discovery Team 57 | *Report, Sep 2024* 58 | [![](https://img.shields.io/badge/report-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://chaiassets.com/chai-1/paper/technical_report_v1.pdf) 59 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/chaidiscovery/chai-lab/) 60 | ![Stars](https://img.shields.io/github/stars/chaidiscovery/chai-lab?color=yellow&style=social) 61 | 62 | **AlphaFold3 Open-Source Implementation (Ligo)** 63 | Edward Harris, Emily Egerton-Warburton, Arda Goreci 64 | *Project, Sep 2024* 65 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/Ligo-Biosciences/AlphaFold3) 66 | ![Stars](https://img.shields.io/github/stars/Ligo-Biosciences/AlphaFold3?color=yellow&style=social) 67 | 68 | 69 | 🔥**Accurate structure prediction of biomolecular interactions with AlphaFold 3** 70 | Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger, Lindsay Willmore, Andrew J. Ballard, Joshua Bambrick, Sebastian W. Bodenstein, David A. Evans, Chia-Chun Hung, Michael O’Neill, David Reiman, Kathryn Tunyasuvunakool, Zachary Wu, Akvilė Žemgulytė, Eirini Arvaniti, Charles Beattie, Ottavia Bertolli, Alex Bridgland, Alexey Cherepanov, Miles Congreve, Alexander I. Cowen-Rivers, Andrew Cowie, Michael Figurnov, Fabian B. Fuchs, Hannah Gladman, Rishub Jain, Yousuf A. Khan, Caroline M. R. Low, Kuba Perlin, Anna Potapenko, Pascal Savy, Sukhdeep Singh, Adrian Stecula, Ashok Thillaisundaram, Catherine Tong, Sergei Yakneen, Ellen D. Zhong, Michal Zielinski, Augustin Žídek, Victor Bapst, Pushmeet Kohli, Max Jaderberg, Demis Hassabis & John M. Jumper 71 | *Nature, May 2024* 72 | [![](https://img.shields.io/badge/nature-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.nature.com/articles/s41586-024-07487-w) 73 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F7572ba7f604ef95d7acdd657ebac458106bd35df%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 74 | [![](https://img.shields.io/badge/news-AB9FF2?style=flat&logo=temporal&labelColor=555555)](https://blog.google/technology/ai/google-deepmind-isomorphic-alphafold-3-ai-model/) 75 | [![](https://img.shields.io/badge/server-AB9FF2?style=flat&logo=temporal&labelColor=555555)](https://golgi.sandbox.google.com/) 76 | 77 | 🔥**Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom** 78 | Rohith Krishna, Jue Wang, Woody Ahern, Pascal Sturmfels, Preetham Venkatesh, Indrek Kalvet, Gyu Rie Lee, Felix S Morey-Burrows, Ivan Anishchenko, Ian R Humphreys, Ryan McHugh, Dionne Vafeados, Xinting Li, George A Sutherland, Andrew Hitchcock, C Neil Hunter, Minkyung Baek, Frank DiMaio, David Baker 79 | *Science, March 2024* 80 | [![](https://img.shields.io/badge/science-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.science.org/doi/10.1126/science.adl2528) 81 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fbbd97deb6e06fe24c5f20fa85e1f276e3065f99f%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 82 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/baker-laboratory/RoseTTAFold-All-Atom) 83 | ![Stars](https://img.shields.io/github/stars/baker-laboratory/RoseTTAFold-All-Atom?color=yellow&style=social) 84 | 85 | 🔥**A glimpse of the next generation of AlphaFold** 86 | Google DeepMind AlphaFold team and Isomorphic Labs team 87 | *News, Oct 2023* 88 | [![](https://img.shields.io/badge/report-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://storage.googleapis.com/deepmind-media/DeepMind.com/Blog/a-glimpse-of-the-next-generation-of-alphafold/alphafold_latest_oct2023.pdf) 89 | [![](https://img.shields.io/badge/news-AB9FF2?style=flat&logo=temporal&labelColor=555555)](https://deepmind.google/discover/blog/a-glimpse-of-the-next-generation-of-alphafold) 90 | 91 | **The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions** 92 | Zymvol Biomodeling 93 | *Nucleic Acids Research, July 2023* 94 | [![](https://img.shields.io/badge/nucleic_acids_research-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://academic.oup.com/nar/article/51/W1/W298/7151343?login=false) 95 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/lightdock/lightdock) 96 | ![Stars](https://img.shields.io/github/stars/lightdock/lightdock?color=yellow&style=social) 97 | 98 | 99 | 100 | 101 | ## Protein-Ligand Docking 102 | 103 | ### 2025 -- Protein-Ligand 104 | **Fast and Accurate Blind Flexible Docking** 105 | Zizhuo Zhang, Lijun Wu, Kaiyuan Gao, Jiangchao Yao, Tao Qin, Bo Han 106 | *ICLR, Jan. 2025* 107 | [![](https://img.shields.io/badge/ICLR-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=iezDdA9oeB) 108 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/resistzzz/FABFlex) 109 | ![Stars](https://img.shields.io/github/stars/resistzzz/FABFlex?color=yellow&style=social) 110 | ![](https://img.shields.io/badge/flexible--blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 111 | 112 | ### 2024 -- Protein-Ligand 113 | 114 | **SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein–Ligand Complex Prediction** 115 | Duanhua Cao, Mingan Chen, Runze Zhang, Zhaokun Wang, Manlin Huang, Jie Yu, Xinyu Jiang, Zhehuan Fan, Wei Zhang, Hao Zhou, Xutong Li, Zunyun Fu, Sulin Zhang, Mingyue Zheng 116 | *Nature Methods, Nov 2024* 117 | [![](https://img.shields.io/badge/nature_methods-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.nature.com/articles/s41592-024-02516-y) 118 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F48753fd45da00aa39a4a14841683158f73625d38%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 119 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/CAODH/SurfDock) 120 | ![Stars](https://img.shields.io/github/stars/CAODH/SurfDock?color=yellow&style=social) 121 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 122 | 123 | **QuickBind: A Light-Weight And Interpretable Molecular Docking Model** 124 | Wojtek Treyde, Seohyun Chris Kim, Nazim Bouatta, Mohammed AlQuraishi 125 | *MLCB, Oct 2024* 126 | [![](https://img.shields.io/badge/mlcb-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://proceedings.mlr.press/v261/treyde24a.html) 127 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F0f7d46ba093a7339aa432231252722a6ffc7946a%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 128 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/aqlaboratory/QuickBind) 129 | ![Stars](https://img.shields.io/github/stars/aqlaboratory/QuickBind?color=yellow&style=social) 130 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 131 | 132 | **One-step Structure Prediction and Screening for Protein-Ligand Complexes using Multi-Task Geometric Deep Learning** 133 | Kelei He, Tiejun Dong, Jinhui Wu, Junfeng Zhang 134 | *Preprint, Aug 2024* 135 | [![](https://img.shields.io/badge/arXiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/pdf/2408.11356) 136 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://gitfront.io/r/LigPose/kMWuV4DW6JpE/LigPose4Review/) 137 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 138 | 139 | 140 | **Fully Flexible Molecular Alignment Enables Accurate Ligand Structure Modelling** 141 | Zhihao Wang, Fan Zhou, Zechen Wang, Qiuyue Hu, Yong-Qiang Li, Sheng Wang, Yanjie Wei, Liangzhen Zheng, Weifeng Li, Xiangda Peng 142 | *JCIM, July 2024* 143 | [![](https://img.shields.io/badge/JCIM-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://pubs.acs.org/doi/10.1021/acs.jcim.4c00669) 144 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fbf416a733a88126a3c46b6c28788ba51b22f4846%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 145 | 146 | 147 | **Deep Learning for Protein-Ligand Docking: Are We There Yet?** 148 | Alex Morehead, Nabin Giri, Jian Liu, Jianlin Cheng 149 | *Preprint, May 2024* 150 | [![](https://img.shields.io/badge/arXiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/pdf/2405.14108) 151 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/BioinfoMachineLearning/PoseBench) 152 | ![Stars](https://img.shields.io/github/stars/BioinfoMachineLearning/PoseBench?color=yellow&style=social) 153 | ![](https://img.shields.io/badge/dataset-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 154 | 155 | 156 | **Uni-Mol Docking V2: Towards Realistic and Accurate Binding Pose Prediction** 157 | Eric Alcaide, Zhifeng Gao, Guolin Ke, Yaqi Li, Linfeng Zhang, Hang Zheng, Gengmo Zhou 158 | *Preprint, May 2024* 159 | [![](https://img.shields.io/badge/arXiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/pdf/2405.11769) 160 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fd03bcd5003d5f35d536f9e9b7ae5c4194de93295%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 161 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/dptech-corp/Uni-Mol) 162 | ![Stars](https://img.shields.io/github/stars/dptech-corp/Uni-Mol?color=yellow&style=social) 163 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 164 | 165 | 166 | **CarsiDock: a deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training** 167 | Heng Cai, Chao Shen, Tianye Jian, Xujun Zhang, Tong Chen, Xiaoqi Han, Zhuo Yang, Wei Dang, Chang-Yu Hsieh, Yu Kang, Peichen Pan, Xiangyang Ji, Jianfei Song, Tingjun Hou and Yafeng Deng 168 | *Chemical Science, December 2023* 169 | [![](https://img.shields.io/badge/chemical_science-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://pubs.rsc.org/en/content/articlepdf/2024/sc/d3sc05552c) 170 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F12f90a54c1f94981ba4f129be8b220b4b8282a6b%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 171 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/carbonsilicon-ai/CarsiDock) 172 | ![Stars](https://img.shields.io/github/stars/carbonsilicon-ai/CarsiDock?color=yellow&style=social) 173 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 174 | 175 | **GeoDirDock: Guiding Docking Along Geodesic Paths** 176 | Raúl Miñán, Javier Gallardo, Álvaro Ciudad, Alexis Molina 177 | *Preprint, April 2024* 178 | [![](https://img.shields.io/badge/under_review-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/pdf/2404.06481.pdf) 179 | 180 | **Interformer: An Interaction-Aware Model for Protein-Ligand Docking and Affinity Prediction** 181 | Houtim Lai, Longyue Wang, Ruiyuan Qian, Geyan Ye, Juhong Huang, Fandi Wu, Fang Wu, Xiangxiang Zeng, Wei Liu 182 | *Preprint, April 2024* 183 | [![](https://img.shields.io/badge/under_review-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.researchsquare.com/article/rs-3995849/v1) 184 | 185 | **FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation** 186 | Kaiyuan Gao, Qizhi Pei, Jinhua Zhu, Tao Qin, Kun He, Lijun Wu 187 | *Preprint, April 2024* 188 | [![](https://img.shields.io/badge/arXiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/pdf/2403.20261.pdf) 189 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F6594ec85ba41682c2ae0b2c205a92ec372f0ec4b%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 190 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/QizhiPei/FABind) 191 | ![Stars](https://img.shields.io/github/stars/QizhiPei/FABind?color=yellow&style=social) 192 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 193 | 194 | **ArtiDock: fast and accurate machine learning approach to protein-ligand docking based on multimodal data augmentation** 195 | Taras Voitsitskyi, Semen Yesylevskyy, Volodymyr Bdzhola, Roman Stratiichuk, Ihor Koleiev, Zakhar Ostrovsky, Volodymyr Vozniak, Ivan Khropachov, Pavlo Henitsoi, Leonid Popryho, Roman Zhytar, Alan Nafiiev, Serhii Starosyla 196 | *Preprint, March 2024* 197 | [![](https://img.shields.io/badge/biorxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.biorxiv.org/content/10.1101/2024.03.14.585019) 198 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fad788c56812bea808f4cb5c31f208a6347f1d24d%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 199 | [![](https://img.shields.io/badge/news-AB9FF2?style=flat&logo=temporal&labelColor=555555)](https://www.biopharmatrend.com/post/713-artidock-from-receptorai-next-generation-ai-docking-that-beats-diffdock-and-alphafold-latest) 200 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 201 | 202 | **Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge** 203 | Yufei Huang, Odin Zhang, Lirong Wu, Cheng Tan, Haitao Lin, Zhangyang Gao, Siyuan Li, Stan. Z. Li 204 | *Preprint, February 2024* 205 | [![](https://img.shields.io/badge/arxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/pdf/2402.11459.pdf) 206 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F68981c9aba4c06176f3c062b94c3e6861371bdb6%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 207 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 208 | ![](https://img.shields.io/badge/flexible-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 209 | 210 | **PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking** 211 | Runze Zhang, Xinyu Jiang, Duanhua Cao, Jie Yu, Mingan Chen, Zhehuan Fan, Xiangtai Kong, Jiacheng Xiong, Zimei Zhang, Wei Zhang, Shengkun Ni, Yitian Wang, Shenghua Gao, Mingyue Zheng 212 | *Preprint, February 2024* 213 | [![](https://img.shields.io/badge/biorxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.biorxiv.org/content/10.1101/2024.01.31.578200v1.full.pdf) 214 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F770f53f09f541b96d0e3693ae4066b897ef9d9f5%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 215 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/Zhang-Runze/PackDock) 216 | ![Stars](https://img.shields.io/github/stars/Zhang-Runze/PackDock?color=yellow&style=social) 217 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 218 | ![](https://img.shields.io/badge/flexible-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 219 | 220 | **State-specific protein–ligand complex structure prediction with a multiscale deep generative model** 221 | Zhuoran Qiao, Weili Nie, Arash Vahdat, Thomas F. Miller II, Animashree Anandkumar 222 | *Nature Machine Intelligence, February 2024* 223 | [![](https://img.shields.io/badge/nature-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.nature.com/articles/s42256-024-00792-z) 224 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fc9561b15c25ca781ccf1a384e978e28341bac0e4%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 225 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/zrqiao/NeuralPLexer) 226 | ![Stars](https://img.shields.io/github/stars/zrqiao/NeuralPLexer?color=yellow&style=social) 227 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 228 | ![](https://img.shields.io/badge/flexible-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 229 | 230 | **DynamicBind: Predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model** 231 | Wei Lu, Jixian Zhang, Huang Weifeng, Ziqiao Zhang, Chengtao Li, Shuangjia Zheng 232 | *Nature Communications, February 2024* 233 | [![](https://img.shields.io/badge/nature-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.nature.com/articles/s41467-024-45461-2) 234 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F51894ffcf778630e7b021bc473d13d028a3b9158%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 235 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/luwei0917/DynamicBind) 236 | ![Stars](https://img.shields.io/github/stars/luwei0917/DynamicBind?color=yellow&style=social) 237 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 238 | ![](https://img.shields.io/badge/flexible-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 239 | 240 | **Deep confident steps to new pockets: strategies for docking generalization** 241 | Gabriele Corso, Arthur Deng, Nicholas Polizzi, Regina Barzilay, Tommi S. Jaakkola 242 | *ICLR, Feburary 2024* 243 | [![](https://img.shields.io/badge/iclr-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=UfBIxpTK10) 244 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fa2af79d2c6a75919d586590487cc3b39b42a94c2%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 245 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/LDeng0205/confidence-bootstrapping) 246 | ![Stars](https://img.shields.io/github/stars/LDeng0205/confidence-bootstrapping?color=yellow&style=social) 247 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 248 | 249 | **(NeuralMD) A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics** 250 | Shengchao Liu, Weitao Du, Yanjing Li, Zhuoxinran Li, Vignesh Bhethanabotla, Nakul Rampal, Omar Yaghi, Christian Borgs, Anima Anandkumar, Hongyu Guo, Jennifer Chayes 251 | *Preprint, January 2024* 252 | [![](https://img.shields.io/badge/arxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/pdf/2401.15122.pdf) 253 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F0215dd9f346534bf4c4247220501d7ab7d7715c6%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 254 | ![](https://img.shields.io/badge/dynamics-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 255 | 256 | ### 2023 -- Protein-Ligand 257 | **(DeltaDock) Multi-scale Iterative Refinement towards Robust and Versatile Molecular Docking** 258 | Jiaxian Yan, Zaixi Zhang, Kai Zhang, Qi Liu 259 | *Preprint, December 2023* 260 | [![](https://img.shields.io/badge/arxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/abs/2311.18574) 261 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fbedc29f7b553bd322df265e2c5a215f1dfd19b4e%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 262 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 263 | 264 | **DiffBindFR: An SE(3) Equivariant Network for Flexible Protein-Ligand Docking** 265 | Jintao Zhu, Zhonghui Gu, Jianfeng Pei, Luhua Lai 266 | *Preprint, November 2023* 267 | [![](https://img.shields.io/badge/biorxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/pdf/2311.15201.pdf) 268 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F04911aa5c3b5d6d07507a0079ebbe6c504a462ae%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 269 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/HBioquant/DiffBindFR) 270 | ![Stars](https://img.shields.io/github/stars/HBioquant/DiffBindFR?color=yellow&style=social) 271 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 272 | ![](https://img.shields.io/badge/flexible-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 273 | 274 | **Structure prediction of protein-ligand complexes from sequence information with Umol** 275 | Patrick Bryant, Atharva Kelkar, Andrea Guljas, Cecilia Clementi, Frank Noé 276 | *Preprint, November 2023* 277 | [![](https://img.shields.io/badge/biorxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://pubmed.ncbi.nlm.nih.gov/37745556/) 278 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F3660911f955c532c186de3b52b03396c851c0aac%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 279 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/patrickbryant1/Umol) 280 | ![Stars](https://img.shields.io/github/stars/patrickbryant1/Umol?color=yellow&style=social) 281 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 282 | 283 | **(FlexPose) Equivariant Flexible Modeling of the Protein–Ligand Binding Pose with Geometric Deep Learning** 284 | Tiejun Dong, Ziduo Yang, Jun Zhou, and Calvin Yu-Chian Chen 285 | *JCTC, November 2023* 286 | [![](https://img.shields.io/badge/jctc-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://pubs.acs.org/doi/full/10.1021/acs.jctc.3c00273) 287 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Ff2633ad706a8537bd7d8d89561d4bbad71373380%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 288 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/tiejundong/FlexPose) 289 | ![Stars](https://img.shields.io/github/stars/tiejundong/FlexPose?color=yellow&style=social) 290 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 291 | ![](https://img.shields.io/badge/flexible-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 292 | 293 | **Pre-Training on Large-Scale Generated Docking Conformations with HelixDock to Unlock the Potential of Protein-ligand Structure Prediction Models** 294 | Lihang Liu, Shanzhuo Zhang, Donglong He, Xianbin Ye, Jingbo Zhou, Xiaonan Zhang, Yaoyao Jiang, Weiming Diao, Hang Yin, Hua Chai, Fan Wang, Jingzhou He, Liang Zheng, Yonghui Li, Xiaomin Fang 295 | *Preprint, October 2023* 296 | [![](https://img.shields.io/badge/arxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/abs/2310.13913) 297 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fe0b05305ce09e20d64394753ac2eca2f7aaf7d9d%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 298 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/molecular_docking/helixdock) 299 | ![Stars](https://img.shields.io/github/stars/PaddlePaddle/PaddleHelix?color=yellow&style=social) 300 | 301 | **PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences** 302 | Martin Buttenschoen, Garrett M. Morris, Charlotte M. Deane 303 | *Preprint, October 2023.* 304 | [![](https://img.shields.io/badge/arxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/abs/2308.05777) 305 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fdd267334c01365d362ed8239394f0ad61b41e269%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 306 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/maabuu/posebusters) 307 | ![Stars](https://img.shields.io/github/stars/maabuu/posebusters?color=yellow&style=social) 308 | ![](https://img.shields.io/badge/dataset-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 309 | 310 | **FABind: Fast and Accurate Protein-Ligand Binding** 311 | Qizhi Pei, Kaiyuan Gao, Lijun Wu, Jinhua Zhu, Yingce Xia, Shufang Xie, Tao Qin, Kun He, Tie-Yan Liu, Rui Yan 312 | *NeurIPS, September 2023* 313 | [![](https://img.shields.io/badge/neurips-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=PnWakgg1RL) 314 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fef5fceee2925cb8441bf1de100b67a33eeeef3a3%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 315 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/QizhiPei/FABind) 316 | ![Stars](https://img.shields.io/github/stars/QizhiPei/FABind?color=yellow&style=social) 317 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 318 | 319 | **Efficient and accurate large library ligand docking with KarmaDock** 320 | Xujun Zhang, Odin Zhang, Chao Shen, Wanglin Qu, Shicheng Chen, Hanqun Cao, Yu Kang, Zhe Wang, Ercheng Wang, Jintu Zhang, Yafeng Deng, Furui Liu, Tianyue Wang, Hongyan Du, Langcheng Wang, Peichen Pan, Guangyong Chen, Chang-Yu Hsieh, Tingjun Hou 321 | *Nature Computational Science, September 2023* 322 | [![](https://img.shields.io/badge/nature-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://doi.org/10.1038/s43588-023-00511-5) 323 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F190320029c58f7e3c1ce8fa9b908d3c88a27df2f%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 324 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/schrojunzhang/KarmaDock) 325 | ![Stars](https://img.shields.io/github/stars/schrojunzhang/KarmaDock?color=yellow&style=social) 326 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 327 | 328 | **(EDM-Dock) Deep Learning Model for Efficient Protein–Ligand Docking with Implicit Side-Chain Flexibility** 329 | Matthew R. Masters, Amr H. Mahmoud, Yao Wei, and Markus A. Lill 330 | *JCIM, March 2023* 331 | [![](https://img.shields.io/badge/nature-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://doi.org/10.1038/s43588-023-00511-5) 332 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fb29d66e1c466bd248232eee0d987118b258fb18e%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 333 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/MatthewMasters/EDM-Dock) 334 | ![Stars](https://img.shields.io/github/stars/MatthewMasters/EDM-Dock?color=yellow&style=social) 335 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 336 | ![](https://img.shields.io/badge/flexible-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 337 | 338 | **Do deep learning models really outperform traditional approaches in molecular docking?** 339 | Yuejiang Yu, Shuqi Lu, Zhifeng Gao, Hang Zheng, Guolin Ke 340 | *ICLR workshop MLDD, March 2023* 341 | [![](https://img.shields.io/badge/iclr_workshop-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=JrtHZdbGtN) 342 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F6fd91f8c48b273bb6c256d5ed4e250edd1b156fa%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 343 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 344 | 345 | 🔥**DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking** 346 | Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi Jaakkola 347 | *ICLR, Feburary 2023* 348 | [![](https://img.shields.io/badge/iclr-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=kKF8_K-mBbS) 349 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F6f0d0b897d0e0963204719b80a8af43ca0d79d90%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 350 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/gcorso/DiffDock) 351 | ![Stars](https://img.shields.io/github/stars/gcorso/DiffDock?color=yellow&style=social) 352 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 353 | 354 | **Uni-Mol: A Universal 3D Molecular Representation Learning Framework** 355 | Gengmo Zhou, Zhifeng Gao, Qiankun Ding, Hang Zheng, Hongteng Xu, Zhewei Wei, Linfeng Zhang, Guolin Ke 356 | *ICLR, Feburary 2023* 357 | [![](https://img.shields.io/badge/iclr-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=6K2RM6wVqKu) 358 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F11f42721f56f36a64638677ccde7784040829656%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 359 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/dptech-corp/Uni-Mol) 360 | ![Stars](https://img.shields.io/github/stars/dptech-corp/Uni-Mol?color=yellow&style=social) 361 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 362 | 363 | **E3Bind: An End-to-End Equivariant Network for Protein-Ligand Docking** 364 | Yangtian Zhang, Huiyu Cai, Chence Shi, Jian Tang 365 | *ICLR, Feburary 2023* 366 | [![](https://img.shields.io/badge/iclr-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=sO1QiAftQFv) 367 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F7cfc990d89875342528b760a4ffed9de47010b03%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 368 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 369 | 370 | ### 2022 -- Protein-Ligand 371 | 372 | **TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction** 373 | Wei Lu, Qifeng Wu, Jixian Zhang, Jiahua Rao, Chengtao Li, Shuangjia Zheng 374 | *NeurIPS, November 2022* 375 | [![](https://img.shields.io/badge/neurips-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=MSBDFwGYwwt) 376 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fb886797dc34c91f186629403d7c7e2092fc25083%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 377 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/luwei0917/TankBind) 378 | ![Stars](https://img.shields.io/github/stars/luwei0917/TankBind?color=yellow&style=social) 379 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 380 | 381 | **EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction** 382 | Hannes Stärk, Octavian Ganea, Lagnajit Pattanaik, Dr.Regina Barzilay, Tommi Jaakkola 383 | *ICML, July 2022* 384 | [![](https://img.shields.io/badge/neurips-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://proceedings.mlr.press/v162/stark22b.html) 385 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F5309f4bcb15e3dafbed759488551c1650b55dd81%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 386 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/HannesStark/EquiBind) 387 | ![Stars](https://img.shields.io/github/stars/HannesStark/EquiBind?color=yellow&style=social) 388 | ![](https://img.shields.io/badge/blind-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 389 | 390 | ## Protein-Protein Docking 391 | ### 2024 -- Protein-Protein 392 | **Deep Reinforcement Learning for Modelling Protein Complexes** 393 | Ziqi Gao, Tao Feng, Jiaxuan You, Chenyi Zi, Yan Zhou, Chen Zhang, Jia Li 394 | *ICLR, March 2024* 395 | [![](https://img.shields.io/badge/iclr-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/pdf/2405.02299) 396 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F5301ef92d5d9d5f2ae0771db8e5b1ea66ea96788%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 397 | ![](https://img.shields.io/badge/assembly-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 398 | 399 | **Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data** 400 | Wei Zheng, Qiqige Wuyun, Yang Li, Chengxin Zhang, P. Lydia Freddolino, Yang Zhang 401 | *Nature Methods, January 2024* 402 | [![](https://img.shields.io/badge/nature-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.nature.com/articles/s41592-023-02130-4) 403 | [![](https://img.shields.io/badge/deepmsa2-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://zhanggroup.org/DeepMSA) 404 | [![](https://img.shields.io/badge/dmfold-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://zhanggroup.org/DMFold) 405 | 406 | **Neural Probabilistic Protein-Protein Docking via a Differentiable Energy Model** 407 | Huaijin Wu, Wei Liu, Yatao Bian, Jiaxiang Wu, Nianzu Yang, Junchi Yan 408 | *ICLR, March 2024* 409 | [![](https://img.shields.io/badge/iclr-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=qg2boc2AwU) 410 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/wuhuaijin/EBMDock) 411 | ![Stars](https://img.shields.io/github/stars/wuhuaijin/EBMDock?color=yellow&style=social) 412 | ![](https://img.shields.io/badge/rigid-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 413 | 414 | **Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction** 415 | Ziyang Yu, Wenbing Huang, Yang Liu 416 | *ICLR, March 2024* 417 | [![](https://img.shields.io/badge/iclr-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=zgQ0PHeGnL) 418 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F7868daf3774809e652f83914fb7b44e36a78d7f2%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 419 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/yaledeus/ElliDock) 420 | ![Stars](https://img.shields.io/github/stars/yaledeus/ElliDock?color=yellow&style=social) 421 | ![](https://img.shields.io/badge/rigid-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 422 | 423 | ### 2023 -- Protein-Protein 424 | **(GeoDock) Flexible protein–protein docking with a multitrack iterative transformer** 425 | Lee-Shin Chu, Jeffrey A. Ruffolo, Ameya Harmalkar, Jeffrey J. Gray 426 | *Protein Science, December 2023* 427 | [![](https://img.shields.io/badge/prosci-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://onlinelibrary.wiley.com/doi/epdf/10.1002/pro.4862) 428 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F1c8af104ce6af12952581007aa19baa63f663a8f%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 429 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/Graylab/GeoDock) 430 | ![Stars](https://img.shields.io/github/stars/Graylab/GeoDock?color=yellow&style=social) 431 | 432 | **Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15** 433 | Jian Liu, Zhiye Guo, Tianqi Wu, Rajashree Roy, Farhan Quadir, Chen Chen, Jianlin Cheng 434 | *Communications Biology, November 2023* 435 | [![](https://img.shields.io/badge/Communications_Biology-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.nature.com/articles/s42003-023-05525-3) 436 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F679d7389ab657a666d0149cfad9ce3b62ee50870%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 437 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/BioinfoMachineLearning/MULTICOM3) 438 | ![Stars](https://img.shields.io/github/stars/BioinfoMachineLearning/MULTICOM3?color=yellow&style=social) 439 | ![](https://img.shields.io/badge/add--on_for_alphafold-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 440 | 441 | **DockGame: Cooperative Games for Multimeric Rigid Protein Docking** 442 | Vignesh Ram Somnath, Pier Giuseppe Sessa, Maria Rodriguez Martinez, Andreas Krause 443 | *Preprint, October 2023* 444 | [![](https://img.shields.io/badge/arXiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://arxiv.org/abs/2310.06177) 445 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F0a76e5107737cd3017a880f52b91ccade4504bf3%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 446 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/vsomnath/dockgame) 447 | ![Stars](https://img.shields.io/github/stars/vsomnath/dockgame?color=yellow&style=social) 448 | ![](https://img.shields.io/badge/rigid-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 449 | ![](https://img.shields.io/badge/multimeric-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 450 | 451 | **Diffdock-pp: Rigid protein-protein docking with diffusion models** 452 | Mohamed Amine Ketata, Cedrik Laue, Ruslan Mammadov, Hannes Stärk, Menghua Wu, Gabriele Corso, Céline Marquet, Regina Barzilay, Tommi S. Jaakkola 453 | *ICLR workshop MLDD, March 2023* 454 | [![](https://img.shields.io/badge/iclr_workshop-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=AM7WbQxuRS) 455 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F345eb3195aac43eb5dcaacc0a7fd288be0fa4491%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 456 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/ketatam/DiffDock-PP) 457 | ![Stars](https://img.shields.io/github/stars/ketatam/DiffDock-PP?color=yellow&style=social) 458 | ![](https://img.shields.io/badge/rigid-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 459 | 460 | **Deep Learning for Flexible and Site-Specific Protein Docking and Design** 461 | Matthew McPartlon, Jinbo Xu 462 | *BioRxiv, April 2023* 463 | [![](https://img.shields.io/badge/bioRxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.biorxiv.org/content/10.1101/2023.04.01.535079) 464 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F663d7f9d2b4b8fcbb488fdb07a7458f734e62726%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 465 | ![](https://img.shields.io/badge/flexible-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 466 | ![](https://img.shields.io/badge/known--pocket-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 467 | 468 | ### 2022 -- Protein-Protein 469 | **Physics-informed deep neural network for rigid-body protein docking** 470 | Freyr Sverrisson, Jean Feydy, Joshua Southern, Michael M Bronstein, Bruno E Correia 471 | *ICLR workshop MLDD, April 2022* 472 | [![](https://img.shields.io/badge/iclr_workshop-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=5yn5shS6wN) 473 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F59f1e3f333f85db9294658ccfe7f0a5f6a9458bd%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 474 | ![](https://img.shields.io/badge/rigid-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 475 | 476 | **Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking** 477 | Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne, Yatao Bian, Regina Barzilay, Tommi S. Jaakkola, Andreas Krause 478 | *ICLR, January 2022* 479 | [![](https://img.shields.io/badge/iclr-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://openreview.net/forum?id=GQjaI9mLet) 480 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fb190df7856f71856cbd98e1394c6513df279d53e%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 481 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/octavian-ganea/equidock_public) 482 | ![Stars](https://img.shields.io/github/stars/octavian-ganea/equidock_public?color=yellow&style=social) 483 | ![](https://img.shields.io/badge/rigid-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 484 | 485 | ### 2021 -- Protein-Protein 486 | 🔥**Protein complex prediction with AlphaFold-Multimer** 487 | Richard Evans, Michael O’Neill, A. Pritzel, Natasha Antropova, Andrew Senior, Tim Green, Augustin Zídek, Russ Bates, Sam Blackwell, Jason Yim, O. Ronneberger, S. Bodenstein, Michal Zielinski, Alex Bridgland, Anna Potapenko, Andrew Cowie, Kathryn Tunyasuvunakool, Rishub Jain, Ellen Clancy, Pushmeet Kohli, J. Jumper, D. Hassabis 488 | *BioRxiv, October 2021* 489 | [![](https://img.shields.io/badge/bioRxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.biorxiv.org/content/10.1101/2021.10.04.463034) 490 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F2556e820cba6bda75f6f31b76bc74d9e36d72cb3%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 491 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/google-deepmind/alphafold) 492 | ![Stars](https://img.shields.io/github/stars/google-deepmind/alphafold?color=yellow&style=social) 493 | ![](https://img.shields.io/badge/flexible-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 494 | 495 | ## Protein-Nucleic Acid Docking 496 | ### 2023 -- Protein-Nucleic Acid 497 | 498 | 🔥**Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA** 499 | Minkyung Baek, Ryan McHugh, Ivan Anishchenko, Hanlun Jiang, David Baker, Frank DiMaio 500 | *Nature Methods, November 2023* 501 | [![](https://img.shields.io/badge/nature-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.nature.com/articles/s41592-023-02086-5) 502 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F0c0ad28901d1cae2cc6c7b9c1f66e9e46afc5ec5%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 503 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/uw-ipd/RoseTTAFold2NA) 504 | ![Stars](https://img.shields.io/github/stars/uw-ipd/RoseTTAFold2NA?color=yellow&style=social) 505 | 506 | **EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks** 507 | Rahmatullah Roche, Bernard Moussad, Md Hossain Shuvo, Sumit Tarafder, Debswapna Bhattacharya 508 | *BioRxiv, September 2023* 509 | [![](https://img.shields.io/badge/bioRxiv-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.biorxiv.org/search/Protein-Nucleic%252BAcid%252B) 510 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/Bhattacharya-Lab/EquiPNAS) 511 | ![Stars](https://img.shields.io/github/stars/Bhattacharya-Lab/EquiPNAS?color=yellow&style=social) 512 | ![](https://img.shields.io/badge/language_model-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 513 | 514 | **Evaluating native-like structures of RNA-protein complexes through the deep learning method** 515 | Chengwei Zeng, Yiren Jian, Soroush Vosoughi, Chen Zeng, Yunjie Zhao 516 | *Nature Communications, February 2023* 517 | [![](https://img.shields.io/badge/nature-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.nature.com/articles/s41467-023-36720-9) 518 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F43253ab8bfa9f19c18764fdcfb550395f5cdfc75%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 519 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/Zhaolab-GitHub/DRPScore_v1.0) 520 | ![Stars](https://img.shields.io/github/stars/Zhaolab-GitHub/DRPScore_v1.0?color=yellow&style=social) 521 | ![](https://img.shields.io/badge/evaluation-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 522 | 523 | 524 | ## Covalent Docking 525 | 526 | **Cov_DOX: A Method for Structure Prediction of Covalent Protein–Ligand Bindings** 527 | Lin Wei, Yaru Chen, Jiaqi Liu, Li Rao, Yanliang Ren, Xin Xu, Jian Wan 528 | *Journal of Medicinal Chemistry, March 2022* 529 | [![](https://img.shields.io/badge/Medicinal_Chemistry-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://pubs.acs.org/doi/full/10.1021/acs.jmedchem.1c02007) 530 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2FURL%3Ahttps%3A%2F%2Fwww.semanticscholar.org%2Fpaper%2FCov_DOX%253A-A-Method-for-Structure-Prediction-of-Wei-Chen%2Fec80310e4d4a9f0308963e1cfccbd624d9fde2da%2F%3Ffields%3DcitationCount&query=citationCount&style=social&label=Citation&labelColor=555555&color=ED8936) 531 | ![](https://img.shields.io/badge/non--cov_based-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 532 | 533 | **CovPDB: a high-resolution coverage of the covalent protein–ligand interactome** 534 | Mingjie Gao, Aurelien F. A. Moumbock, Ammar Qaseem, Qianqing Xu, Stefan Gunther 535 | *Nucleic Acids Research, September 2021* 536 | [![](https://img.shields.io/badge/Nucleic_Acids_Res.-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://academic.oup.com/nar/article/50/D1/D445/6377397) 537 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2FURL%3Ahttps%3A%2F%2Fwww.semanticscholar.org%2Fpaper%2FCovPDB%253A-a-high-resolution-coverage-of-the-covalent-Gao-Moumbock%2Fa800cdd78504470a4b8c3a5fd31879a249686676%2F%3Ffields%3DcitationCount&query=citationCount&style=social&label=Citation&labelColor=555555&color=ED8936) 538 | [![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://drug-discovery.vm.uni-freiburg.de/covpdb/) 539 | ![](https://img.shields.io/badge/dataset-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 540 | 541 | **Fragment-based covalent ligand discovery** 542 | Wenchao Lu, Milka Kostic, Tinghu Zhang, Jianwei Che, Matthew P. Patricelli, Lyn H. Jones, Edward T. Chouchaniae, Nathanael S. Gray 543 | *RSC Chemical Biology, February 2021* 544 | [![](https://img.shields.io/badge/RSC_Chemical_Biology-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://pubs.rsc.org/en/content/articlelanding/2021/CB/D0CB00222D) 545 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2FURL%3Ahttps%3A%2F%2Fwww.semanticscholar.org%2Fpaper%2FFragment-based-covalent-ligand-discovery-Lu-Kostic%2Fb525ba2c0b80e4587f2b1c6f667cf0009a46b356%2F%3Ffields%3DcitationCount&query=citationCount&style=social&label=Citation&labelColor=555555&color=ED8936) 546 | ![](https://img.shields.io/badge/hybrid_method-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 547 | 548 | **Covalent docking of large libraries for the discovery of chemical probes** 549 | Nir London, Rand M Miller, Shyam Krishnan, Kenji Uchida, John J Irwin, Oliv Eidam, Lucie Gibold, Peter Cimermančič, Richard Bonnet, Brian K Shoichet, Jack Taunton 550 | *Nature Chemical Biology, September 2014* 551 | [![](https://img.shields.io/badge/Nature_Chemical_Biology-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4232467/) 552 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2FURL%3Ahttps%3A%2F%2Fwww.semanticscholar.org%2Fpaper%2FCovalent-Docking-of-Large-Libraries-for-the-of-London-Miller%2F90211028d92ba511542f8b1ccdbdbc7720e6710a%2F%3Ffields%3DcitationCount&query=citationCount&style=social&label=Citation&labelColor=555555&color=ED8936) 553 | [![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://drug-discovery.vm.uni-freiburg.de/covpdb/) 554 | ![](http://covalent.docking.org/) 555 | ![](https://img.shields.io/badge/non--cov_based-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 556 | 557 | **Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring** 558 | Kai Zhu, Kenneth W. Borrelli, Jeremy R. Greenwood, Tyler Day, Robert Abel, Ramy S. Farid, and Edward Harder 559 | *Journal of Chemical Information and Modeling, June 2014* 560 | [![](https://img.shields.io/badge/Chemical_Information_and_Modeling-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://pubs.acs.org/doi/10.1021/ci500118s) 561 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2FURL%3Ahttps%3A%2F%2Fwww.semanticscholar.org%2Fpaper%2FDocking-Covalent-Inhibitors%253A-A-Parameter-Free-To-Zhu-Borrelli%2F2d9998235f41a9b9ef91cde87dc1bab05b194592%2F%3Ffields%3DcitationCount&query=citationCount&style=social&label=Citation&labelColor=555555&color=ED8936) 562 | ![](https://img.shields.io/badge/parameter_free-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 563 | 564 | **CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints** 565 | Xuchang Ouyang, Shuo Zhou, Chinh Tran To Su, Zemei Ge, Runtao Li, Chee Keong Kwoh 566 | *Journal of Computational Chemistry, February 2013* 567 | [![](https://img.shields.io/badge/Computational_Chemistry-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://onlinelibrary.wiley.com/doi/10.1002/jcc.23136) 568 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2FURL%3Ahttps%3A%2F%2Fwww.semanticscholar.org%2Fpaper%2FCovalentDock%253A-Automated-covalent-docking-with-and-Ouyang-Zhou%2F13e5c154c51d9d9950b8eca7668d4e83b957c1ae%2F%3Ffields%3DcitationCount&query=citationCount&style=social&label=Citation&labelColor=555555&color=ED8936) 569 | [![](https://img.shields.io/badge/project-38C26D?style=flat&logo=googlecloud&labelColor=555555)](https://code.google.com/archive/p/covalentdock/) 570 | ![](https://img.shields.io/badge/Autodock_based-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 571 | 572 | ## Survey 573 | ### Protein-Ligand 574 | 575 | **Machine-learning methods for ligand–protein molecular docking** 576 | Kevin Crampon, Alexis Giorkallos, Myrtille Deldossi, Stéphanie Baud, Luiz Angelo Steffenel 577 | *Drug Discovery Today, January 2022* 578 | [![](https://img.shields.io/badge/drugdis-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.sciencedirect.com/science/article/abs/pii/S1359644621003974) 579 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F790e0a160fff355ce2fbb51beb4362dfcc58a830%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 580 | 581 | **A practical guide to large-scale docking** 582 | Brian J. Bender, Stefan Gahbauer, Andreas Luttens, Jiankun Lyu, Chase M. Webb, Reed M. Stein, Elissa A. Fink, Trent E. Balius, Jens Carlsson, John J. Irwin & Brian K. Shoichet 583 | *Nature Protocols, December 2021* 584 | [![](https://img.shields.io/badge/natureprotocols-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.nature.com/articles/s41596-021-00597-z) 585 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F31a2f29489f4a95ed85f8ffb854de758e8be4c09%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 586 | 587 | **An Overview of Scoring Functions Used for Protein–Ligand Interactions in Molecular Docking** 588 | Jin Li, Ailing Fu, Le Zhang 589 | *Interdisciplinary Sciences: Computational Life Sciences, March 2019* 590 | [![](https://img.shields.io/badge/InterSciComLifeSci-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://link.springer.com/article/10.1007/s12539-019-00327-w) 591 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F7eaa28830e31289a102084653654c3f911f05413%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 592 | 593 | **Progress in molecular docking** 594 | Jiyu Fan, Ailing Fu, Le Zhang 595 | *Quantitative Biology, June 2019* 596 | [![](https://img.shields.io/badge/QuantBio-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://link.springer.com/article/10.1007/s40484-019-0172-y) 597 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F3c8b953cccb19a0a1679c28f73b33df20b2fd10e%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 598 | 599 | **Molecular Docking: Shifting Paradigms in Drug Discovery** 600 | Luca Pinzi, Giulio Rastelli 601 | *International Journal of Molecular Sciences, September 2019* 602 | [![](https://img.shields.io/badge/ijms-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.mdpi.com/1422-0067/20/18/4331) 603 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F8f7948d72b19b3be7191396c5e637cdb14a2371c%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 604 | 605 | **From machine learning to deep learning: Advances in scoring functions for protein–ligand docking** 606 | Chao Shen, Junjie Ding, Zhe Wang, Dongsheng Cao, Xiaoqin Ding, Tingjun Hou 607 | *WIREs computational molecular science, June 2019* 608 | [![](https://img.shields.io/badge/ComMolSci-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://wires.onlinelibrary.wiley.com/doi/abs/10.1002/wcms.1429) 609 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F9a297e83ca2bf1b3af089e51d85e927544ddfe04%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 610 | 611 | **Software for molecular docking: a review** 612 | Nataraj S. Pagadala, Khajamohiddin Syed, Jack Tuszynski 613 | *Biophysical Reviews, January 2017* 614 | [![](https://img.shields.io/badge/BioReview-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://link.springer.com/article/10.1007/s12551-016-0247-1) 615 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fcd6e2fde7c80146a5f42bbe4e3638951e796ce0a%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 616 | 617 | **Dynamic Docking: A Paradigm Shift in Computational Drug Discovery** 618 | Gioia, Dario, Martina Bertazzo, Maurizio Recanatini, Matteo Masetti, Andrea Cavalli 619 | *Molecules, November 2017* 620 | [![](https://img.shields.io/badge/Molecules-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.mdpi.com/1420-3049/22/11/2029) 621 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F49d40250c1bf1eb95b5c8caa3c2f663f336f117d%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 622 | 623 | **Insights into Protein–Ligand Interactions: Mechanisms, Models, and Methods** 624 | Xing Du, Yi Li, Yuan-Ling Xia, Shi-Meng Ai, Jing Liang, Peng Sang, Xing-Lai Ji, Shu-Qun Liu 625 | *International Journal of Molecular Sciences, January 2016* 626 | [![](https://img.shields.io/badge/MolSci-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.mdpi.com/1422-0067/17/2/144) 627 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fbfd1b11cf32a063a7deec39ec0d76232f365582a%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 628 | 629 | ### Protein-Protein 630 | 631 | **Protein–Protein Docking: Past, Present, and Future** 632 | Sharon Sunny, PB Jayaraj 633 | *The protein journal, February 2022* 634 | [![](https://img.shields.io/badge/PROTEINJ-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://link.springer.com/article/10.1007/s10930-021-10031-8) 635 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F60d7599aef518716e447853f0fa0cdafa774eabb%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 636 | 637 | **A survey on computational models for predicting protein–protein interactions** 638 | Lun Hu, Xiaojuan Wang, Yu-An Huang, Pengwei Hu, Zhu-Hong You 639 | *Briefings in Bioinformatics, September 2021* 640 | [![](https://img.shields.io/badge/BriefBioinform-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://academic.oup.com/bib/article/22/5/bbab036/6159365) 641 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F171b6d5c35ac3cda7a821bff4041f360bee20e54%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 642 | 643 | **What method to use for protein–protein docking?** 644 | Kathryn Porter, Israel Desta, Dima Kozakov, Sandor Vajda 645 | *Current Opinion in Structural Biology, April 2019* 646 | [![](https://img.shields.io/badge/CURROPINSTRUCBIOL-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.sciencedirect.com/science/article/abs/pii/S0959440X18300691) 647 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2F5098ef6ab4fbf1b5a7b180fd91cddac231abfd85%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 648 | 649 | ### Protein-Nucleic Acid 650 | 651 | **Challenges in structural modeling of RNA-protein interactions** 652 | Xudong Liu, Yingtian Duan, Xu Hong, Juan Xie, Shiyong Liu 653 | *Current Opinion in Structural Biology, June 2023* 654 | [![](https://img.shields.io/badge/StructuralBiology-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://www.sciencedirect.com/science/article/pii/S0959440X23000970) 655 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fb56c2784e1154c86541ee16b1aaeacfc6a46a321%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 656 | 657 | **Protein–RNA interaction prediction with deep learning: structure matters** 658 | Junkang Wei, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li 659 | *Briefings in Bioinformatics， January 2022* 660 | [![](https://img.shields.io/badge/BrefInBio-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://academic.oup.com/bib/article/23/1/bbab540/6470965) 661 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2Fd8eb3568107b21787751cd6c25776aacfa991979%3Ffields%3DcitationCount&query=%24.citationCount&label=citation&style=social&labelColor=555555&color=ED8936) 662 | 663 | ### Covalent 664 | 665 | **Docking covalent targets for drug discovery: stimulating the computer-aided drug design community of possible pitfalls and erroneous practices** 666 | Abdul-Quddus Kehinde Oyedele, Abdeen Tunde Ogunlana, Ibrahim Damilare Boyenle, Ayodeji Oluwadamilare Adeyemi, Temionu Oluwakemi Rita, Temitope Isaac Adelusi, Misbaudeen Abdul-Hammed, Oluwabamise Emmanuel Elegbeleye, Tope Tunji Odunitan 667 | *Molecular Diversity, September 2022* 668 | [![](https://img.shields.io/badge/Molecular_Diversity-5291C8?style=flat&logo=Read.cv&labelColor=555555)](https://link.springer.com/article/10.1007/s11030-022-10523-4) 669 | ![Dynamic JSON Badge](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fapi.semanticscholar.org%2Fgraph%2Fv1%2Fpaper%2FURL%3Ahttps%3A%2F%2Fwww.semanticscholar.org%2Fpaper%2FDocking-covalent-targets-for-drug-discovery%253A-the-of-Oyedele-Ogunlana%2Ff347739ce3bbe75cf8bebe42aebbed12d4d9da6c%2F%3Ffields%3DcitationCount&query=citationCount&style=social&label=Citation&labelColor=555555&color=ED8936) 670 | 671 | ## Traditional Docking Tools 672 | ### Open-source and free access 673 | 674 | - **Smina** 675 | [![](https://img.shields.io/badge/source_forge-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://sourceforge.net/projects/smina) 676 | - 🔥**AutoDock Suite** 677 | [![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://ccsb.scripps.edu/projects/docking) 678 | [![](https://img.shields.io/badge/AutoDock_Vina-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/ccsb-scripps/AutoDock-Vina/releases) 679 | ![Stars](https://img.shields.io/github/stars/ccsb-scripps/AutoDock-Vina?color=yellow&style=social) 680 | - **AutoDock-GPU** 681 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/ccsb-scripps/AutoDock-GPU) 682 | ![Stars](https://img.shields.io/github/stars/ccsb-scripps/AutoDock-GPU?color=yellow&style=social) 683 | - **MGLTools software suite** 684 | [![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://ccsb.scripps.edu/mgltools/) 685 | ![](https://img.shields.io/badge/free--access-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 686 | - **SwissDock** 687 | [![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](http://www.swissdock.ch/) 688 | ![](https://img.shields.io/badge/free--access-FD6F6F?style=flat&logo=darkreader&labelColor=555555&logocolor=555555) 689 | - **rDock** 690 | [![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://rdock.github.io) 691 | [![](https://img.shields.io/badge/code-38C26D?style=flat&logo=GitHub&labelColor=555555)](https://github.com/CBDD/rDock) 692 | ![Stars](https://img.shields.io/github/stars/CBDD/rDock?color=yellow&style=social) 693 | 694 | ### Commercial tool 695 | 696 | - **GOLD Suite** 697 | [![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://www.ch.cam.ac.uk/computing/software/gold-suite) 698 | - **GLIDE** 699 | [![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://www.schrodinger.com/products/glide) 700 | - **MOE-Dock** 701 | [![](https://img.shields.io/badge/website-AB9FF2?style=flat&logo=temporal&labelColor=555555&logocolor=555555)](https://www.computabio.com/molecular-docking-service.html) 702 | 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