DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

4 October 2022

Papers citing "DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking"

41 / 41 papers shown

Title
Piloting Structure-Based Drug Design via Modality-Specific Optimal Schedule Keyue Qiu Yuxuan Song Zhehuan Fan Peidong Liu Z. Zhang Mingyue Zheng Hao Zhou Wei-Ying Ma 26 0 0 12 May 2025
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 42 0 0 03 May 2025
All-atom Diffusion Transformers: Unified generative modelling of molecules and materials Chaitanya K. Joshi Xiang Fu Yi-Lun Liao Vahe Gharakhanyan Benjamin Kurt Miller Anuroop Sriram Zachary W. Ulissi DiffM 53 4 0 05 Mar 2025
Non-Linear Flow Matching for Full-Atom Peptide Design Dengdeng Huang Shikui Tu 36 0 0 21 Feb 2025
Open Materials Generation with Stochastic Interpolants Philipp Hoellmer Thomas Egg Maya M. Martirossyan Eric Fuemmeler Amit Gupta ... George Karypis Mark K. Transtrum Richard G. Hennig E. Tadmor Stefano Martiniani AI4CE 90 0 0 04 Feb 2025
Group Ligands Docking to Protein Pockets Jiaqi Guan Jiahan Li Xiangxin Zhou Xingang Peng Sheng Wang Yunan Luo Jian-wei Peng Jianzhu Ma 33 0 0 28 Jan 2025
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction Alex Morehead Jianlin Cheng OOD 112 2 0 14 Dec 2024
Beyond Autoregression: Discrete Diffusion for Complex Reasoning and Planning Jiacheng Ye Jiahui Gao Shansan Gong Lin Zheng Xin Jiang Z. Li Lingpeng Kong DiffM LRM 46 15 0 18 Oct 2024
MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks N. Kim Seongsu Kim Minsu Kim Jinkyoo Park Sungsoo Ahn AI4CE 41 0 0 07 Oct 2024
Generative Topological Networks Alona Levy-Jurgenson Z. Yakhini 38 0 0 21 Jun 2024
Evaluating representation learning on the protein structure universe Arian R. Jamasb Alex Morehead Chaitanya K. Joshi Zuobai Zhang Kieran Didi ... Charles Harris Jian Tang Jianlin Cheng Pietro Lio Tom L. Blundell SSL 38 12 0 19 Jun 2024
Cometh: A continuous-time discrete-state graph diffusion model Antoine Siraudin Fragkiskos D. Malliaros Christopher Morris 31 3 0 10 Jun 2024
Grounding Continuous Representations in Geometry: Equivariant Neural Fields David R. Wessels David M. Knigge Samuele Papa Riccardo Valperga Sharvaree P. Vadgama E. Gavves Erik J. Bekkers 40 7 0 09 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
Diffusion On Syntax Trees For Program Synthesis Shreyas Kapur Erik Jenner Stuart J. Russell DiffM 32 5 0 30 May 2024
CHAMP: Conformalized 3D Human Multi-Hypothesis Pose Estimators Harry Zhang Luca Carlone 3DH 66 1 0 27 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
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design Amit Kadan Kevin Ryczko Erika Lloyd A. Roitberg Takeshi Yamazaki 85 1 0 20 May 2024
ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering Yiqing Shen Outongyi Lv Houying Zhu Yu Guang Wang 33 4 0 21 Apr 2024
FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation Kaiyuan Gao Qizhi Pei Jinhua Zhu Kun He Lijun Wu Lijun Wu 34 6 0 29 Mar 2024
A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications Jiaqi Han Jiacheng Cen Liming Wu Zongzhao Li Xiangzhe Kong ... Zhewei Wei Deli Zhao Yu Rong Wenbing Huang Wenbing Huang AI4CE 34 20 0 01 Mar 2024
Deep Confident Steps to New Pockets: Strategies for Docking Generalization Gabriele Corso Arthur Deng Benjamin Fry Nicholas Polizzi Regina Barzilay Tommi Jaakkola OOD 37 27 0 28 Feb 2024
Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure Ian Dunn D. Koes DiffM GNN 19 3 0 22 Nov 2023
Closed-Form Diffusion Models Christopher Scarvelis Haitz Sáez de Ocáriz Borde Justin Solomon DiffM 95 9 0 19 Oct 2023
DockGame: Cooperative Games for Multimeric Rigid Protein Docking Vignesh Ram Somnath Pier Giuseppe Sessa María Rodríguez Martínez Andreas Krause 34 2 0 09 Oct 2023
DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces Michael S. Jones Kirill Shmilovich Andrew L. Ferguson DiffM 34 12 0 23 Jul 2023
Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learning Shuxin Zheng Jiyan He Chang-Shu Liu Yu Shi Ziheng Lu ... Peiran Jin Chi Chen Frank Noé Haiguang Liu Tie-Yan Liu AI4CE 19 40 0 08 Jun 2023
Accurate transition state generation with an object-aware equivariant elementary reaction diffusion model Chenru Duan Yuanqi Du Haojun Jia Heather J. Kulik DiffM 26 46 0 12 Apr 2023
Graph Representation Learning for Interactive Biomolecule Systems Xinye Xiong Bingxin Zhou Yu Guang Wang AI4CE GNN 33 0 0 05 Apr 2023
DDP: Diffusion Model for Dense Visual Prediction Yuanfeng Ji Zhe Chen Enze Xie Lanqing Hong Xihui Liu Zhaoqiang Liu Tong Lu Zhenguo Li Ping Luo DiffM VLM 47 130 0 30 Mar 2023
Aligned Diffusion Schrödinger Bridges Vignesh Ram Somnath Matteo Pariset Ya-Ping Hsieh María Rodríguez Martínez Andreas Krause Charlotte Bunne DiffM 117 30 0 22 Feb 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 41 50 0 17 Feb 2023
How to Trust Your Diffusion Model: A Convex Optimization Approach to Conformal Risk Control Jacopo Teneggi Matthew Tivnan J. W. Stayman Jeremias Sulam DiffM 30 28 0 07 Feb 2023
Implicit Convolutional Kernels for Steerable CNNs Maksim Zhdanov Nico Hoffmann Gabriele Cesa 26 5 0 12 Dec 2022
Neural Cell Video Synthesis via Optical-Flow Diffusion Manuel Serna-Aguilera Khoa Luu Nathaniel Harris Min Zou DiffM VGen 23 1 0 06 Dec 2022
Fast Graph Generation via Spectral Diffusion Tianze Luo Zhanfeng Mo Sinno Jialin Pan DiffM 13 22 0 16 Nov 2022
An optimal control perspective on diffusion-based generative modeling Julius Berner Lorenz Richter Karen Ullrich DiffM 28 80 0 02 Nov 2022
Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing Yuanqi Du Charles Harris Arian R. Jamasb Ilia Igashov ... Pietro Lió Carla P. Gomes Max Welling Michael M. Bronstein B. Correia DiffM 31 193 0 24 Oct 2022
Structure-based drug design with geometric deep learning Clemens Isert Kenneth Atz G. Schneider 38 104 0 19 Oct 2022
State-specific protein-ligand complex structure prediction with a multi-scale deep generative model Zhuoran Qiao Weili Nie Arash Vahdat Thomas F. Miller Anima Anandkumar DiffM 31 84 0 30 Sep 2022
Riemannian Score-Based Generative Modelling Valentin De Bortoli Emile Mathieu M. Hutchinson James Thornton Yee Whye Teh Arnaud Doucet DiffM 222 164 0 06 Feb 2022