Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds

29 January 2023

Mohammed AlQuraishi

Papers citing "Generating Novel, Designable, and Diverse Protein Structures by Equivariantly Diffusing Oriented Residue Clouds"

31 / 31 papers shown

Title
ProtPainter: Draw or Drag Protein via Topology-guided Diffusion Zhengxi Lu Shizhuo Cheng Yuru Jiang Yan Zhang M. Zhang DiffM 24 0 0 19 Apr 2025
Proteina: Scaling Flow-based Protein Structure Generative Models Tomas Geffner Kieran Didi Zuobai Zhang Danny Reidenbach Zhonglin Cao ... Mario Geiger Christian Dallago E. Küçükbenli Arash Vahdat Karsten Kreis DiffM AI4CE 41 4 0 02 Mar 2025
Learning conformational ensembles of proteins based on backbone geometry Nicolas Wolf Leif Seute Vsevolod Viliuga Simon Wagner Jan Stühmer Frauke Gräter AI4CE 45 0 0 19 Feb 2025
On Diffusion Posterior Sampling via Sequential Monte Carlo for Zero-Shot Scaffolding of Protein Motifs James Matthew Young O. Deniz Akyildiz DiffM 75 1 0 08 Dec 2024
ProteinWeaver: A Divide-and-Assembly Approach for Protein Backbone Design Yiming Ma Fei Ye Yi Zhou Zaixiang Zheng Dongyu Xue Quanquan Gu 56 0 0 08 Nov 2024
DPLM-2: A Multimodal Diffusion Protein Language Model X. Wang Zaixiang Zheng Fei Ye Dongyu Xue Shujian Huang Quanquan Gu 20 13 0 17 Oct 2024
Generative Modeling of Molecular Dynamics Trajectories Bowen Jing Hannes Stärk Tommi Jaakkola Bonnie Berger AI4CE 27 14 0 26 Sep 2024
Latent Diffusion Models for Controllable RNA Sequence Generation Kaixuan Huang Yukang Yang Kaidi Fu Yanyi Chu Le Cong Mengdi Wang 39 1 0 15 Sep 2024
ProteinBench: A Holistic Evaluation of Protein Foundation Models Fei Ye Zaixiang Zheng Dongyu Xue Yuning Shen Lihao Wang Yiming Ma Yan Wang X. Wang Xiangxin Zhou Quanquan Gu ELM 25 6 0 10 Sep 2024
RNA-FrameFlow: Flow Matching for de novo 3D RNA Backbone Design Rishabh Anand Chaitanya K. Joshi Alex Morehead Arian R. Jamasb Charles Harris Simon V. Mathis Kieran Didi Bryan Hooi Pietro Liò Pietro Liò 42 2 0 19 Jun 2024
Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules Trevor Norton Debswapna Bhattacharya MedIm DiffM 29 2 0 31 May 2024
Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation Guillaume Huguet James Vuckovic Kilian Fatras Eric Thibodeau-Laufer Pablo Lemos ... Jarrid Rector-Brooks Tara Akhound-Sadegh Michael M. Bronstein Alexander Tong A. Bose 32 26 0 30 May 2024
Out of Many, One: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2 Yeqing Lin Minji Lee Zhao Zhang Mohammed AlQuraishi DiffM 27 17 0 24 May 2024
De novo antibody design with SE(3) diffusion Daniel Cutting Frédéric A. Dreyer David Errington Constantin Schneider Charlotte M. Deane DiffM 25 3 0 13 May 2024
PPFlow: Target-aware Peptide Design with Torsional Flow Matching Haitao Lin Odin Zhang Huifeng Zhao Dejun Jiang Lirong Wu Zicheng Liu Yufei Huang Stan Z. Li 39 12 0 05 Mar 2024
TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation Zongying Lin Hao Li Liuzhenghao Lv Lin Bin Junwu Zhang Calvin Yu-Chian Chwn Li Yuan Tian Yonghong 19 3 0 27 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 14 24 0 13 Feb 2024
Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion Alex Morehead Jeffrey A. Ruffolo Aadyot Bhatnagar Ali Madani DiffM 17 9 0 21 Dec 2023
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design Kieran Didi Francisco Vargas Simon V. Mathis Vincent Dutordoir Emile Mathieu U. J. Komorowska Pietro Lió DiffM 25 13 0 14 Dec 2023
Inverse folding for antibody sequence design using deep learning Frédéric A. Dreyer Daniel Cutting Constantin Schneider Henry Kenlay Charlotte M. Deane 11 14 0 30 Oct 2023
Generative artificial intelligence for de novo protein design Adam Winnifrith C. Outeiral Brian L. Hie AI4CE 24 13 0 15 Oct 2023
Functional Geometry Guided Protein Sequence and Backbone Structure Co-Design Justin Dumouchelle Yunlong Zhao Wenxian Shi Yang Yang Lei Li 8 2 0 06 Oct 2023
Ophiuchus: Scalable Modeling of Protein Structures through Hierarchical Coarse-graining SO(3)-Equivariant Autoencoders Allan dos Santos Costa Ilan Mitnikov Mario Geiger Manvitha Ponnapati Tess E. Smidt Joseph Jacobson DiffM 10 3 0 04 Oct 2023
SE(3)-Stochastic Flow Matching for Protein Backbone Generation A. Bose Tara Akhound-Sadegh Guillaume Huguet Kilian Fatras Jarrid Rector-Brooks Cheng-Hao Liu A. Nica Maksym Korablyov Michael M. Bronstein Alexander Tong DiffM 22 71 0 03 Oct 2023
AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies Karolis Martinkus J. Ludwiczak Kyunghyun Cho Weishao Lian J. Lafrance-Vanasse ... A. Rajpal Y. Wu Richard Bonneau Vladimir Gligorijević Andreas Loukas DiffM 19 36 0 28 Jul 2023
Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling Jiarui Lu Bozitao Zhong Zuobai Zhang Jian Tang 14 24 0 05 Jun 2023
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing Yang Zhang Zuobai Zhang Bozitao Zhong Sanchit Misra Jian Tang DiffM 14 31 0 01 Jun 2023
A Latent Diffusion Model for Protein Structure Generation Cong Fu Keqiang Yan Limei Wang Wing Yee Au Michael McThrow Tao Komikado Koji Maruhashi Kanji Uchino Xiaoning Qian Shuiwang Ji DiffM 8 31 0 06 May 2023
Protein structure generation via folding diffusion Kevin E. Wu Kevin Kaichuang Yang Rianne van den Berg James Y. Zou Alex X. Lu Ava P. Amini DiffM 17 189 0 30 Sep 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 23 84 0 30 Sep 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 175 170 0 26 May 2022