A framework for conditional diffusion modelling with applications in
motif scaffolding for protein design

A framework for conditional diffusion modelling with applications in motif scaffolding for protein design

14 December 2023

Francisco Vargas

Simon V. Mathis

Vincent Dutordoir

U. J. Komorowska

Papers citing "A framework for conditional diffusion modelling with applications in motif scaffolding for protein design"

12 / 12 papers shown

Title
MotifBench: A standardized protein design benchmark for motif-scaffolding problems Zhuoqi Zheng Bo Zhang Kieran Didi Kevin K. Yang Jason Yim Joseph L. Watson Hai-Feng Chen Brian L. Trippe 43 1 0 20 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
On conditional diffusion models for PDE simulations Aliaksandra Shysheya Cristiana-Diana Diaconu Federico Bergamin P. Perdikaris José Miguel Hernández-Lobato Richard E. Turner Emile Mathieu DiffM 23 0 0 21 Oct 2024
Physics-aligned Schrödinger bridge Zeyu Li Hongkun Dou Shen Fang Wang Han Yue Deng Lijun Yang AI4CE DiffM 20 0 0 26 Sep 2024
TFG: Unified Training-Free Guidance for Diffusion Models Haotian Ye Haowei Lin Jiaqi Han Minkai Xu Sheng Liu Yitao Liang Jianzhu Ma James Zou Stefano Ermon 19 13 0 24 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 33 2 0 19 Jun 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 22 2 0 24 May 2024
Improved motif-scaffolding with SE(3) flow matching Jason Yim Andrew Campbell Emile Mathieu Andrew Y. K. Foong Michael Gastegger ... Victor Garcia Satorras Bastiaan S. Veeling Frank Noé Regina Barzilay Tommi Jaakkola 13 31 0 08 Jan 2024
Score-based Data Assimilation François Rozet Gilles Louppe 29 32 0 18 Jun 2023
gRNAde: Geometric Deep Learning for 3D RNA inverse design Chaitanya K. Joshi Arian R. Jamasb Ramón Viñas Charles Harris Simon V. Mathis Alex Morehead Rishabh Anand Pietro Lió 8 13 0 24 May 2023
RePaint: Inpainting using Denoising Diffusion Probabilistic Models Andreas Lugmayr Martin Danelljan Andrés Romero F. I. F. Richard Yu Radu Timofte Luc Van Gool DiffM 200 1,330 0 24 Jan 2022
Zero-Shot Text-to-Image Generation Aditya A. Ramesh Mikhail Pavlov Gabriel Goh Scott Gray Chelsea Voss Alec Radford Mark Chen Ilya Sutskever VLM 253 4,735 0 24 Feb 2021