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Structure-based Drug Design with Equivariant Diffusion Models

Structure-based Drug Design with Equivariant Diffusion Models

24 October 2022
Arne Schneuing
Yuanqi Du
Charles Harris
Arian R. Jamasb
Ilia Igashov
Weitao Du
Tom L. Blundell
Pietro Lió
Carla P. Gomes
Max Welling
Michael M. Bronstein
B. Correia
    DiffM
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Papers citing "Structure-based Drug Design with Equivariant Diffusion Models"

50 / 116 papers shown
Title
A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization
A 3D pocket-aware and evolutionary conserved interaction guided diffusion model for molecular optimization
Anjie Qiao
Hao Zhang
Qianmu Yuan
Qirui Deng
Jingtian Su
W. R. Huang
Huihao Zhou
Guo-Bo Li
Z. Wang
J. Lei
DiffM
14
0
0
09 May 2025
A 3D pocket-aware and affinity-guided diffusion model for lead optimization
A 3D pocket-aware and affinity-guided diffusion model for lead optimization
Anjie Qiao
Junjie Xie
W. R. Huang
Hao Zhang
Jiahua Rao
Shuangjia Zheng
Yuedong Yang
Z. Wang
Guo-Bo Li
J. Lei
DiffM
MedIm
28
0
0
29 Apr 2025
AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification
AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification
Maximilian G. Schuh
Joshua Hesse
Stephan A. Sieber
23
1
0
15 Apr 2025
FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation
FLOWR: Flow Matching for Structure-Aware De Novo, Interaction- and Fragment-Based Ligand Generation
Julian Cremer
Ross Irwin
Alessandro Tibot
J. Janet
Simon Olsson
Djork-Arné Clevert
24
0
0
14 Apr 2025
Compositional Flows for 3D Molecule and Synthesis Pathway Co-design
Compositional Flows for 3D Molecule and Synthesis Pathway Co-design
Tony Shen
Seonghwan Seo
Ross Irwin
Kieran Didi
Simon Olsson
Woo Youn Kim
Martin Ester
34
0
0
10 Apr 2025
A Comprehensive Benchmark for RNA 3D Structure-Function Modeling
A Comprehensive Benchmark for RNA 3D Structure-Function Modeling
Luis Wyss
Vincent Mallet
Wissam Karroucha
Karsten M. Borgwardt
Carlos G. Oliver
36
0
0
27 Mar 2025
TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design
TransDiffSBDD: Causality-Aware Multi-Modal Structure-Based Drug Design
Xiuyuan Hu
Guoqing Liu
Can Chen
Yang Zhao
Hao Zhang
Xue Liu
42
2
0
26 Mar 2025
Concept-Driven Deep Learning for Enhanced Protein-Specific Molecular Generation
Taojie Kuang
Qianli Ma
Athanasios V. Vasilakos
Yu Wang
Qiang
Cheng
Zhixiang Ren
38
0
0
11 Mar 2025
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
Xiangxin Zhou
Yi Xiao
Haowei Lin
Xinheng He
Jiaqi Guan
Yang Wang
Qiang Liu
F. I. S. Kevin Zhou
Liang Wang
Jianzhu Ma
AI4CE
45
0
0
06 Mar 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
42
3
0
05 Mar 2025
Symmetry-Preserving Diffusion Models via Target Symmetrization
Symmetry-Preserving Diffusion Models via Target Symmetrization
Vinh Tong
Yun Ye
Trung-Dung Hoang
Anji Liu
Guy Van den Broeck
Mathias Niepert
DiffM
72
0
0
17 Feb 2025
Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance
Ziqi Chen
B. Peng
Tianhua Zhai
Daniel Adu-Ampratwum
Xia Ning
50
1
0
09 Feb 2025
BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation
Ali Khodabandeh Yalabadi
Mehdi Yazdani-Jahromi
O. Garibay
33
0
0
28 Jan 2025
Score-based 3D molecule generation with neural fields
Score-based 3D molecule generation with neural fields
Matthieu Kirchmeyer
Pedro H. O. Pinheiro
Saeed Saremi
DiffM
40
0
0
15 Jan 2025
Unified Guidance for Geometry-Conditioned Molecular Generation
Unified Guidance for Geometry-Conditioned Molecular Generation
Sirine Ayadi
Leon Hetzel
Johanna Sommer
Fabian J. Theis
Stephan Günnemann
28
0
0
05 Jan 2025
Exploring Discrete Flow Matching for 3D De Novo Molecule Generation
Exploring Discrete Flow Matching for 3D De Novo Molecule Generation
Ian Dunn
D. Koes
76
4
0
25 Nov 2024
SEE-DPO: Self Entropy Enhanced Direct Preference Optimization
SEE-DPO: Self Entropy Enhanced Direct Preference Optimization
Shivanshu Shekhar
Shreyas Singh
Tong Zhang
25
4
0
06 Nov 2024
ET-SEED: Efficient Trajectory-Level SE(3) Equivariant Diffusion Policy
ET-SEED: Efficient Trajectory-Level SE(3) Equivariant Diffusion Policy
Chenrui Tie
Yue Chen
Ruihai Wu
Boxuan Dong
Z. Li
Chongkai Gao
Hao Dong
35
3
0
06 Nov 2024
Diffusion Twigs with Loop Guidance for Conditional Graph Generation
Diffusion Twigs with Loop Guidance for Conditional Graph Generation
Giangiacomo Mercatali
Yogesh Verma
André Freitas
Vikas K. Garg
24
3
0
31 Oct 2024
Reprogramming Pretrained Target-Specific Diffusion Models for
  Dual-Target Drug Design
Reprogramming Pretrained Target-Specific Diffusion Models for Dual-Target Drug Design
Xiangxin Zhou
Jiaqi Guan
Y. Zhang
Xingang Peng
Liang Wang
Jianzhu Ma
16
0
0
28 Oct 2024
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models
Kiwoong Yoo
Owen Oertell
Junhyun Lee
Sanghoon Lee
Jaewoo Kang
28
0
0
28 Oct 2024
Bio2Token: All-atom tokenization of any biomolecular structure with Mamba
Bio2Token: All-atom tokenization of any biomolecular structure with Mamba
Andrew Liu
Axel Elaldi
Nathan Russell
Olivia Viessmann
Mamba
58
2
0
24 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance
Chemistry-Inspired Diffusion with Non-Differentiable Guidance
Yuchen Shen
Chenhao Zhang
Sijie Fu
Chenghui Zhou
Newell Washburn
Barnabás Póczos
43
0
0
09 Oct 2024
DiffGAD: A Diffusion-based Unsupervised Graph Anomaly Detector
DiffGAD: A Diffusion-based Unsupervised Graph Anomaly Detector
Jinghan Li
Yuan Gao
Jinda Lu
Junfeng Fang
Congcong Wen
Hui Lin
Xiang Wang
37
0
0
09 Oct 2024
Generative Flows on Synthetic Pathway for Drug Design
Generative Flows on Synthetic Pathway for Drug Design
Seonghwan Seo
Minsu Kim
Tony Shen
Martin Ester
Jinkyoo Park
Sungsoo Ahn
Woo Youn Kim
35
2
0
06 Oct 2024
Task-agnostic Pre-training and Task-guided Fine-tuning for Versatile Diffusion Planner
Task-agnostic Pre-training and Task-guided Fine-tuning for Versatile Diffusion Planner
Chenyou Fan
Chenjia Bai
Zhao Shan
Haoran He
Yang Zhang
Zhen Wang
18
3
0
30 Sep 2024
Instruction-Based Molecular Graph Generation with Unified Text-Graph
  Diffusion Model
Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model
Yuran Xiang
Haiteng Zhao
Chang Ma
Zhi-Hong Deng
26
0
0
19 Aug 2024
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much?
What Ails Generative Structure-based Drug Design: Expressivity is Too Little or Too Much?
Rafał Karczewski
Samuel Kaski
Markus Heinonen
Vikas K. Garg
25
0
0
12 Aug 2024
Decomposed Direct Preference Optimization for Structure-Based Drug
  Design
Decomposed Direct Preference Optimization for Structure-Based Drug Design
Xiwei Cheng
Xiangxin Zhou
Yuwei Yang
Yu Bao
Quanquan Gu
23
3
0
19 Jul 2024
AIGC for Industrial Time Series: From Deep Generative Models to Large Generative Models
AIGC for Industrial Time Series: From Deep Generative Models to Large Generative Models
Lei Ren
Haiteng Wang
Yang Tang
Yang Tang
Chunhua Yang
AI4TS
AI4CE
25
4
0
16 Jul 2024
EquiBot: SIM(3)-Equivariant Diffusion Policy for Generalizable and Data
  Efficient Learning
EquiBot: SIM(3)-Equivariant Diffusion Policy for Generalizable and Data Efficient Learning
Jingyun Yang
Zi-ang Cao
Congyue Deng
Rika Antonova
Shuran Song
Jeannette Bohg
DiffM
36
2
0
01 Jul 2024
Molecular Diffusion Models with Virtual Receptors
Molecular Diffusion Models with Virtual Receptors
Matan Halfon
Eyal Rozenberg
Ehud Rivlin
Daniel Freedman
32
0
0
26 Jun 2024
General Binding Affinity Guidance for Diffusion Models in
  Structure-Based Drug Design
General Binding Affinity Guidance for Diffusion Models in Structure-Based Drug Design
Yue Jian
Curtis Wu
Danny Reidenbach
Aditi S. Krishnapriyan
27
1
0
24 Jun 2024
Efficient Evolutionary Search Over Chemical Space with Large Language Models
Efficient Evolutionary Search Over Chemical Space with Large Language Models
Haorui Wang
Marta Skreta
C. Ser
Wenhao Gao
Lingkai Kong
...
Yanqiao Zhu
Yuanqi Du
Alán Aspuru-Guzik
Kirill Neklyudov
Chao Zhang
37
10
0
23 Jun 2024
Evaluating representation learning on the protein structure universe
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
23
12
0
19 Jun 2024
Evaluating the design space of diffusion-based generative models
Evaluating the design space of diffusion-based generative models
Yuqing Wang
Ye He
Molei Tao
DiffM
25
1
0
18 Jun 2024
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
Haitao Lin
Guojiang Zhao
Odin Zhang
Yufei Huang
Lirong Wu
Zicheng Liu
Siyuan Li
Cheng Tan
Zhifeng Gao
Stan Z. Li
14
2
0
16 Jun 2024
Lift Your Molecules: Molecular Graph Generation in Latent Euclidean
  Space
Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space
Mohamed Amine Ketata
Nicholas Gao
Johanna Sommer
Tom Wollschlager
Stephan Günnemann
DiffM
21
1
0
15 Jun 2024
Human-level molecular optimization driven by mol-gene evolution
Human-level molecular optimization driven by mol-gene evolution
Jiebin Fang
Churu Mao
Yuchen Zhu
Xiaoming Chen
Chang-Yu Hsieh
Zhongjun Ma
BDL
22
0
0
13 Jun 2024
Diffusion On Syntax Trees For Program Synthesis
Diffusion On Syntax Trees For Program Synthesis
Shreyas Kapur
Erik Jenner
Stuart J. Russell
DiffM
19
5
0
30 May 2024
PILOT: Equivariant diffusion for pocket conditioned de novo ligand
  generation with multi-objective guidance via importance sampling
PILOT: Equivariant diffusion for pocket conditioned de novo ligand generation with multi-objective guidance via importance sampling
Julian Cremer
Tuan Le
Frank Noé
Djork-Arné Clevert
Kristof T. Schütt
DiffM
14
8
0
23 May 2024
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design
Amit Kadan
Kevin Ryczko
Erika Lloyd
A. Roitberg
Takeshi Yamazaki
80
0
0
20 May 2024
Structure-based drug design by denoising voxel grids
Structure-based drug design by denoising voxel grids
Pedro H. O. Pinheiro
Arian R. Jamasb
Omar Mahmood
Vishnu Sresht
Saeed Saremi
DiffM
19
7
0
07 May 2024
SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints
SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints
M. Cretu
Charles Harris
Julien Roy
Emmanuel Bengio
Pietro Lió
Bruno Correia
Julien Roy
Emmanuel Bengio
Pietro Liò
19
1
0
02 May 2024
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule
  Generation
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation
Ian Dunn
D. Koes
BDL
DiffM
36
11
0
30 Apr 2024
A Survey on Diffusion Models for Time Series and Spatio-Temporal Data
A Survey on Diffusion Models for Time Series and Spatio-Temporal Data
Yiyuan Yang
Ming Jin
Haomin Wen
Chaoli Zhang
Yuxuan Liang
...
Bin Yang
Zenglin Xu
Jiang Bian
Shirui Pan
Qingsong Wen
DiffM
AI4TS
SyDa
21
7
0
29 Apr 2024
ControlMol: Adding Substruture Control To Molecule Diffusion Models
ControlMol: Adding Substruture Control To Molecule Diffusion Models
Zhengyang Qi
Zijing Liu
Jiying Zhang
He Cao
Yu Li
33
2
0
22 Apr 2024
An Overview of Diffusion Models: Applications, Guided Generation,
  Statistical Rates and Optimization
An Overview of Diffusion Models: Applications, Guided Generation, Statistical Rates and Optimization
Minshuo Chen
Song Mei
Jianqing Fan
Mengdi Wang
VLM
MedIm
DiffM
24
48
0
11 Apr 2024
AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug
  Design
AUTODIFF: Autoregressive Diffusion Modeling for Structure-based Drug Design
Xinze Li
Penglei Wang
Tianfan Fu
Wenhao Gao
Chengtao Li
Leilei Shi
Junhong Liu
25
2
0
02 Apr 2024
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation
Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation
Odin Zhang
Yufei Huang
Shichen Cheng
Mengyao Yu
Xujun Zhang
...
Yu Kang
Sunliang Cui
P. Pan
Chang-Yu Hsieh
Tingjun Hou
19
4
0
15 Mar 2024
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