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MotifBench: A standardized protein design benchmark for motif-scaffolding problems

MotifBench: A standardized protein design benchmark for motif-scaffolding problems

20 February 2025
Zhuoqi Zheng
Bo Zhang
Kieran Didi
Kevin K. Yang
Jason Yim
Joseph L. Watson
Hai-Feng Chen
Brian L. Trippe
ArXiv (abs)PDFHTML

Papers citing "MotifBench: A standardized protein design benchmark for motif-scaffolding problems"

9 / 9 papers shown
Title
On diffusion posterior sampling via sequential Monte Carlo for zero-shot scaffolding of protein motifs
On diffusion posterior sampling via sequential Monte Carlo for zero-shot scaffolding of protein motifs
James Matthew Young
O. Deniz Akyildiz
DiffM
254
3
0
08 Dec 2024
DPLM-2: A Multimodal Diffusion Protein Language Model
DPLM-2: A Multimodal Diffusion Protein Language ModelInternational Conference on Learning Representations (ICLR), 2024
Xinze Wang
Zaixiang Zheng
Fei Ye
Dongyu Xue
Shujian Huang
Quanquan Gu
230
51
0
17 Oct 2024
Out of Many, One: Designing and Scaffolding Proteins at the Scale of the
  Structural Universe with Genie 2
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
167
42
0
24 May 2024
Improved motif-scaffolding with SE(3) flow matching
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
340
50
0
08 Jan 2024
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
Kieran Didi
Francisco Vargas
Simon Mathis
Vincent Dutordoir
Emile Mathieu
Urszula Julia Komorowska
Pietro Lio
DiffM
446
20
0
14 Dec 2023
Joint Design of Protein Sequence and Structure based on Motifs
Joint Design of Protein Sequence and Structure based on Motifs
Zhenqiao Song
Yunlong Zhao
Yufei Song
Wenxian Shi
Yang Yang
Lei Li
3DVDiffM
128
3
0
04 Oct 2023
Practical and Asymptotically Exact Conditional Sampling in Diffusion
  Models
Practical and Asymptotically Exact Conditional Sampling in Diffusion ModelsNeural Information Processing Systems (NeurIPS), 2023
Luhuan Wu
Brian L. Trippe
C. A. Naesseth
David M. Blei
John P. Cunningham
DiffM
277
157
0
30 Jun 2023
SE(3) diffusion model with application to protein backbone generation
SE(3) diffusion model with application to protein backbone generationInternational Conference on Machine Learning (ICML), 2023
Jason Yim
Brian L. Trippe
Valentin De Bortoli
Emile Mathieu
Arnaud Doucet
Regina Barzilay
Tommi Jaakkola
DiffM
377
279
0
05 Feb 2023
Diffusion probabilistic modeling of protein backbones in 3D for the
  motif-scaffolding problem
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problemInternational Conference on Learning Representations (ICLR), 2022
Brian L. Trippe
Jason Yim
D. Tischer
D. Baker
Tamara Broderick
Regina Barzilay
Tommi Jaakkola
DiffM
283
300
0
08 Jun 2022
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