State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

30 September 2022

Papers citing "State-specific protein-ligand complex structure prediction with a multi-scale deep generative model"

22 / 22 papers shown

Title
PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking Yize Jiang Xinze Li Y. Zhang Jin Han Youjun Xu ... Yejin Choi Wu-Jun Li Tianfan Fu Fang Wu Junhong Liu 40 0 0 03 May 2025
Fast and Accurate Blind Flexible Docking Zizhuo Zhang Lijun Wu Kaiyuan Gao Jiangchao Yao Tao Qin Bo Han 36 0 0 20 Feb 2025
Generative diffusion model with inverse renormalization group flows Kanta Masuki Yuto Ashida DiffM 63 0 0 17 Jan 2025
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction Alex Morehead Jianlin Cheng OOD 112 1 0 14 Dec 2024
Dockformer: A transformer-based molecular docking paradigm for large-scale virtual screening Zhangfan Yang Junkai Ji Shan He Jianqiang Li Ruibin Bai Zexuan Zhu Yew-Soon Ong Y. Ong 28 0 0 11 Nov 2024
QuickBind: A Light-Weight And Interpretable Molecular Docking Model Wojtek Treyde Seohyun Chris Kim N. Bouatta Mohammed AlQuraishi 17 0 0 21 Oct 2024
RapidDock: Unlocking Proteome-scale Molecular Docking Rafał Powalski Bazyli Klockiewicz Maciej Jaśkowski Bartosz Topolski Paweł Dąbrowski-Tumański Maciej Wiśniewski Łukasz Kuciński Piotr Miłoś Dariusz Plewczynski 19 0 0 16 Oct 2024
Assessing interaction recovery of predicted protein-ligand poses David Errington Constantin Schneider Cédric Bouysset Frédéric A. Dreyer AI4CE 15 3 0 30 Sep 2024
Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization Siyi Gu Minkai Xu Alexander Powers Weili Nie Tomas Geffner Karsten Kreis J. Leskovec Arash Vahdat Stefano Ermon 40 7 0 01 Jul 2024
SelfDefend: LLMs Can Defend Themselves against Jailbreaking in a Practical Manner Xunguang Wang Daoyuan Wu Zhenlan Ji Zongjie Li Pingchuan Ma Shuai Wang Yingjiu Li Yang Liu Ning Liu Juergen Rahmel AAML 71 8 0 08 Jun 2024
$Diffusion Models in $\textit{De Novo}$ Drug Design$ Diffusion Models in $\textit{De Novo}$ Drug Design Amira Alakhdar Barnabás Póczos Newell Washburn MedIm 34 13 0 07 Jun 2024
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models Hunter Nisonoff Junhao Xiong Stephan Allenspach Jennifer Listgarten 55 31 0 03 Jun 2024
Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules Trevor Norton Debswapna Bhattacharya MedIm DiffM 40 2 0 31 May 2024
Deep Learning for Protein-Ligand Docking: Are We There Yet? Alex Morehead Nabin Giri Jian Liu Jianlin Cheng Jianlin Cheng OOD 32 4 0 23 May 2024
LLMs Can Defend Themselves Against Jailbreaking in a Practical Manner: A Vision Paper Daoyuan Wu Shuaibao Wang Yang Liu Ning Liu AAML 37 7 0 24 Feb 2024
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge Yufei Huang Odin Zhang Lirong Wu Cheng Tan Haitao Lin Zhangyang Gao Siyuan Li Stan. Z. Li DiffM 17 6 0 18 Feb 2024
Diffusion-based Graph Generative Methods Hongyang Chen Can Xu Lingyu Zheng Qiang Zhang Xuemin Lin DiffM MedIm 20 0 0 28 Jan 2024
Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola 31 25 0 09 Oct 2023
A Systematic Survey in Geometric Deep Learning for Structure-based Drug Design Zaixin Zhang Jiaxian Yan Qi Liu Enhong Chen Marinka Zitnik 30 1 0 20 Jun 2023
A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture Hyun Park Xiaoli Yan Ruijie Zhu Eliu A. Huerta Santanu Chaudhuri Donny Cooper Ian T. Foster E. Tajkhorshid AI4CE 30 18 0 14 Jun 2023
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 130 403 0 04 Oct 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 183 172 0 26 May 2022