Torsional Diffusion for Molecular Conformer Generation

1 June 2022

Papers citing "Torsional Diffusion for Molecular Conformer Generation"

50 / 169 papers shown

Title
PROflow: An iterative refinement model for PROTAC-induced structure prediction Bo Qiang Wenxian Shi Yuxuan Song Menghua Wu 32 1 0 10 Apr 2024
AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design Xinze Li Penglei Wang Tianfan Fu Wenhao Gao Chengtao Li Leilei Shi Junhong Liu 38 2 0 02 Apr 2024
On Diffusion Process in SE(3)-invariant Space Zihan Zhou Ruiying Liu Jiachen Zheng Xiaoxue Wang Tianshu Yu DiffM 32 1 0 03 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 32 20 0 01 Mar 2024
Retrieval-Augmented Generation for AI-Generated Content: A Survey Penghao Zhao Hailin Zhang Qinhan Yu Zhengren Wang Yunteng Geng Fangcheng Fu Ling Yang Wentao Zhang Jie Jiang Bin Cui 3DV 110 220 0 29 Feb 2024
Deep Confident Steps to New Pockets: Strategies for Docking Generalization Gabriele Corso Arthur Deng Benjamin Fry Nicholas Polizzi Regina Barzilay Tommi Jaakkola OOD 30 26 0 28 Feb 2024
Feedback Efficient Online Fine-Tuning of Diffusion Models Masatoshi Uehara Yulai Zhao Kevin Black Ehsan Hajiramezanali Gabriele Scalia N. Diamant Alex Tseng Sergey Levine Tommaso Biancalani 22 21 0 26 Feb 2024
Fine-Tuning of Continuous-Time Diffusion Models as Entropy-Regularized Control Masatoshi Uehara Yulai Zhao Kevin Black Ehsan Hajiramezanali Gabriele Scalia N. Diamant Alex Tseng Tommaso Biancalani Sergey Levine 29 42 0 23 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 24 6 0 18 Feb 2024
Position: Topological Deep Learning is the New Frontier for Relational Learning Theodore Papamarkou Tolga Birdal Michael M. Bronstein Gunnar Carlsson Justin Curry ... Petar Velickovic Bei Wang Yusu Wang Guo-Wei Wei Ghada Zamzmi AI4CE 54 25 0 14 Feb 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 19 25 0 13 Feb 2024
Score-based generative models break the curse of dimensionality in learning a family of sub-Gaussian probability distributions Frank Cole Yulong Lu DiffM 23 6 0 12 Feb 2024
Improved off-policy training of diffusion samplers Marcin Sendera Minsu Kim Sarthak Mittal Pablo Lemos Luca Scimeca Jarrid Rector-Brooks Alexandre Adam Yoshua Bengio Nikolay Malkin OffRL 64 17 0 07 Feb 2024
Diffusion Model-Based Multiobjective Optimization for Gasoline Blending Scheduling Wenxuan Fang Wei Du Renchu He Yang Tang Yaochu Jin Gary G. Yen DiffM 28 5 0 04 Feb 2024
Conditional Normalizing Flows for Active Learning of Coarse-Grained Molecular Representations Henrik Schopmans Pascal Friederich AI4CE 20 1 0 02 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
Generative Model for Constructing Reaction Path from Initial to Final States Akihide Hayashi So Takamoto Ju Li Daisuke Okanohara 15 1 0 19 Jan 2024
Scalable Normalizing Flows Enable Boltzmann Generators for Macromolecules Joseph C. Kim David Bloore Karan Kapoor Jun Feng Ming-Hong Hao Mengdi Wang 37 7 0 08 Jan 2024
Time Series Diffusion Method: A Denoising Diffusion Probabilistic Model for Vibration Signal Generation H. Yi Lei Hou Yuhong Jin N. A. Saeed Ali Kandil Hao Duan DiffM 21 21 0 13 Dec 2023
Spectroscopy-Guided Discovery of Three-Dimensional Structures of Disordered Materials with Diffusion Models H. Kwon Tim Hsu Wenyu Sun Wonseok Jeong Fikret Aydin ... Xiao Chen Matthew R. Carbone Deyu Lu Fei Zhou Tuan Anh Pham DiffM 22 9 0 09 Dec 2023
Equivariant Scalar Fields for Molecular Docking with Fast Fourier Transforms Bowen Jing Tommi Jaakkola Bonnie Berger 13 2 0 07 Dec 2023
Molecule Joint Auto-Encoding: Trajectory Pretraining with 2D and 3D Diffusion Weitao Du Jiujiu Chen Xuecang Zhang Zhiming Ma Shengchao Liu DiffM 25 9 0 06 Dec 2023
Swallowing the Bitter Pill: Simplified Scalable Conformer Generation Yuyang Wang Ahmed A. A. Elhag Navdeep Jaitly J. Susskind Miguel Angel Bautista DiffM 27 19 0 27 Nov 2023
Gradual Optimization Learning for Conformational Energy Minimization Artem Tsypin L. Ugadiarov Kuzma Khrabrov Alexander Telepov Egor Rumiantsev Alexey Skrynnik Aleksandr I. Panov Dmitry Vetrov E. Tutubalina Artur Kadurin 24 1 0 05 Nov 2023
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method Yuyan Ni Shikun Feng Wei-Ying Ma Zhiming Ma Yanyan Lan DiffM AI4CE 27 9 0 03 Nov 2023
Investigating the Behavior of Diffusion Models for Accelerating Electronic Structure Calculations D. Rothchild Andrew S. Rosen Eric Taw Connie Robinson Joseph E. Gonzalez Aditi S. Krishnapriyan DiffM 24 2 0 02 Nov 2023
Scaling Riemannian Diffusion Models Aaron Lou Minkai Xu Stefano Ermon 22 8 0 30 Oct 2023
Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model Shiwei Liu Tian Zhu Milong Ren Chungong Yu Dongbo Bu Haicang Zhang DiffM 22 18 0 30 Oct 2023
Towards equilibrium molecular conformation generation with GFlowNets Alexandra Volokhova Michal Koziarski Alex Hernández-García Cheng-Hao Liu Santiago Miret Pablo Lemos Luca Thiede Zichao Yan Alán Aspuru-Guzik Yoshua Bengio 24 9 0 20 Oct 2023
Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models Gabriele Corso Yilun Xu Valentin De Bortoli Regina Barzilay Tommi Jaakkola DiffM 16 20 0 19 Oct 2023
Reflection-Equivariant Diffusion for 3D Structure Determination from Isotopologue Rotational Spectra in Natural Abundance Austin H. Cheng Alston Lo Santiago Miret Brooks H Pate Alán Aspuru-Guzik 24 6 0 17 Oct 2023
MOFDiff: Coarse-grained Diffusion for Metal-Organic Framework Design Xiang Fu Tian Xie Andrew S. Rosen Tommi Jaakkola Jake A. Smith DiffM 21 9 0 16 Oct 2023
Generative Modeling on Manifolds Through Mixture of Riemannian Diffusion Processes Jaehyeong Jo Sung Ju Hwang DiffM 27 9 0 11 Oct 2023
DockGame: Cooperative Games for Multimeric Rigid Protein Docking Vignesh Ram Somnath Pier Giuseppe Sessa María Rodríguez Martínez Andreas Krause 27 1 0 09 Oct 2023
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
On Accelerating Diffusion-based Molecular Conformation Generation in SE(3)-invariant Space Zihan Zhou Ruiying Liu Tianshu Yu DiffM 30 0 0 07 Oct 2023
Backdiff: a diffusion model for generalized transferable protein backmapping Yikai Liu Ming Chen Guang Lin DiffM 22 2 0 03 Oct 2023
Mirror Diffusion Models for Constrained and Watermarked Generation Guan-Horng Liu T. Chen Evangelos A. Theodorou Molei Tao DiffM 16 21 0 02 Oct 2023
Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation Tuan Le Julian Cremer Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 27 25 0 29 Sep 2023
Beta Diffusion Mingyuan Zhou Tianqi Chen Zhendong Wang Huangjie Zheng DiffM 16 10 0 14 Sep 2023
Molecular Conformation Generation via Shifting Scores Zihan Zhou Ruiying Liu Chaolong Ying Ruimao Zhang Tianshu Yu DiffM 29 2 0 12 Sep 2023
3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation Sungjun Cho Dae-Woong Jeong Sung Moon Ko Jinwoo Kim Sehui Han Seunghoon Hong Honglak Lee Moontae Lee AI4CE DiffM 30 1 0 08 Sep 2023
SE(3) Equivariant Augmented Coupling Flows Laurence I. Midgley Vincent Stimper Javier Antorán Emile Mathieu Bernhard Schölkopf José Miguel Hernández-Lobato 30 22 0 20 Aug 2023
Crystal Structure Prediction by Joint Equivariant Diffusion Rui Jiao Wen-bing Huang Peijia Lin Jiaqi Han Pin Chen Yutong Lu Yang Liu DiffM 16 59 0 30 Jul 2023
DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces Michael S. Jones Kirill Shmilovich Andrew L. Ferguson DiffM 27 12 0 23 Jul 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 38 25 0 20 Jul 2023
Metropolis Sampling for Constrained Diffusion Models N. Fishman Leo Klarner Emile Mathieu M. Hutchinson Valentin De Bortoli DiffM 27 14 0 11 Jul 2023
Towards Symmetry-Aware Generation of Periodic Materials Youzhi Luo Chengkai Liu Shuiwang Ji DiffM 18 21 0 06 Jul 2023
Improved sampling via learned diffusions Lorenz Richter Julius Berner DiffM 24 52 0 03 Jul 2023
Graph Denoising Diffusion for Inverse Protein Folding Kai Yi Bingxin Zhou Yiqing Shen Pietro Lio' Yu Guang Wang DiffM 6 41 0 29 Jun 2023