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Full-Atom Peptide Design based on Multi-modal Flow Matching

Full-Atom Peptide Design based on Multi-modal Flow Matching

2 June 2024
Jiahan Li
Chaoran Cheng
Zuofan Wu
Ruihan Guo
Shitong Luo
Zhizhou Ren
Jian-wei Peng
Jianzhu Ma
ArXiv (abs)PDFHTMLGithub (103★)

Papers citing "Full-Atom Peptide Design based on Multi-modal Flow Matching"

17 / 17 papers shown
Generative design and validation of therapeutic peptides for glioblastoma based on a potential target ATP5A
Generative design and validation of therapeutic peptides for glioblastoma based on a potential target ATP5A
Hao Qian
Pu You
Lin Zeng
Jingyuan Zhou
Dengdeng Huang
Kaicheng Li
Shikui Tu
Lei Xu
107
0
0
19 Nov 2025
Full-Atom Peptide Design via Riemannian-Euclidean Bayesian Flow Networks
Full-Atom Peptide Design via Riemannian-Euclidean Bayesian Flow Networks
Hao Qian
Shikui Tu
L. Xu
152
0
0
18 Nov 2025
Joint Design of Protein Surface and Structure Using a Diffusion Bridge Model
Joint Design of Protein Surface and Structure Using a Diffusion Bridge Model
Guanlue Li
Xufeng Zhao
Fang Wu
Sören Laue
DiffM
147
0
0
08 Nov 2025
ProteinAE: Protein Diffusion Autoencoders for Structure Encoding
ProteinAE: Protein Diffusion Autoencoders for Structure Encoding
Shaoning Li
Le Zhuo
Yusong Wang
Mingyu Li
Xinheng He
Fandi Wu
Jiaming Song
Pheng-Ann Heng
DiffM
155
1
0
12 Oct 2025
Latent Retrieval Augmented Generation of Cross-Domain Protein Binders
Latent Retrieval Augmented Generation of Cross-Domain Protein Binders
Zishen Zhang
Xiangzhe Kong
Wenbing Huang
Yang Liu
DiffM
263
0
0
12 Oct 2025
NS-Pep: De novo Peptide Design with Non-Standard Amino Acids
NS-Pep: De novo Peptide Design with Non-Standard Amino Acids
Tao Guo
Junbo Yin
Yu Wang
Xin Gao
210
0
0
01 Oct 2025
Riemannian Consistency Model
Riemannian Consistency Model
Chaoran Cheng
Yusong Wang
Yuxin Chen
Xiangxin Zhou
Nanning Zheng
Ge Liu
346
3
0
01 Oct 2025
Prior-Guided Flow Matching for Target-Aware Molecule Design with Learnable Atom Number
Prior-Guided Flow Matching for Target-Aware Molecule Design with Learnable Atom Number
Jingyuan Zhou
Hao Qian
Shikui Tu
L. Xu
260
1
0
01 Sep 2025
Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling
Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling
Xiangxin Zhou
Mingyu Li
Yi Xiao
Jiahan Li
Dongyu Xue
Zaixiang Zheng
Jianzhu Ma
Quanquan Gu
256
3
0
27 May 2025
BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design
BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design
Divya Nori
Anisha Parsan
Caroline Uhler
Wengong Jin
226
3
0
27 May 2025
An All-Atom Generative Model for Designing Protein Complexes
An All-Atom Generative Model for Designing Protein Complexes
Ruizhe Chen
Dongyu Xue
Xiangxin Zhou
Zaixiang Zheng
Xiangxiang Zeng
Quanquan Gu
573
10
0
17 Apr 2025
$α$-Flow: A Unified Framework for Continuous-State Discrete Flow Matching Models
ααα-Flow: A Unified Framework for Continuous-State Discrete Flow Matching Models
Chaoran Cheng
Jiahan Li
Jiajun Fan
Ge Liu
349
11
0
14 Apr 2025
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic FlowsInternational Conference on Learning Representations (ICLR), 2025
Xiangxin Zhou
Yi Xiao
Haowei Lin
Xinheng He
Jiaqi Guan
Yang Wang
Qiang Liu
F. I. S. Kevin Zhou
Liang Wang
Jianzhu Ma
AI4CE
314
2
0
06 Mar 2025
THFlow: A Temporally Hierarchical Flow Matching Framework for 3D Peptide Design
THFlow: A Temporally Hierarchical Flow Matching Framework for 3D Peptide Design
Dengdeng Huang
Shikui Tu
488
0
0
21 Feb 2025
Training Free Guided Flow Matching with Optimal Control
Training Free Guided Flow Matching with Optimal ControlInternational Conference on Learning Representations (ICLR), 2024
Luran Wang
Chaoran Cheng
Yizhen Liao
Yanru Qu
Ge Liu
513
18
0
23 Oct 2024
Computational design of target-specific linear peptide binders with
  TransformerBeta
Computational design of target-specific linear peptide binders with TransformerBeta
Haowen Zhao
Francesco A. Aprile
Barbara Bravi
293
0
0
07 Oct 2024
Categorical Flow Matching on Statistical Manifolds
Categorical Flow Matching on Statistical ManifoldsNeural Information Processing Systems (NeurIPS), 2024
Chaoran Cheng
Jiahan Li
Jian-wei Peng
Ge Liu
567
28
0
26 May 2024
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