RosettaCommons/RFdiffusion

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Code for running RFdiffusion

Stars: 3.1k
Forks: 644
Open beginner issues: 0
Indexed issues: 222

Dominant language: Python
License: No license data
Last GitHub push: Jul 15, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

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222 issues indexed so far

Designing a symmetric binder Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

RosettaCommons/RFdiffusion#456 · 3 comments · Opened Jun 8, 2026
Two-sided partial diffusion with sequence gaps? Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

RosettaCommons/RFdiffusion#453 · 1 comment · Opened May 18, 2026
RF diffusion colab- RMSD Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/RFdiffusion#449 · Opened Apr 3, 2026
5070Ti cuda error Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

RosettaCommons/RFdiffusion#444 · 6 comments · Opened Mar 17, 2026
Deformation of coordinate space Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#443 · Opened Feb 24, 2026
Job crash (Segmentation fault) during run Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#442 · Opened Feb 20, 2026
Contradiction between RFD3 design and AF3 prediction Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#440 · 3 comments · Opened Jan 27, 2026
How to make it work properly on CUDA 13 with an RTX 5090? Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

RosettaCommons/RFdiffusion#439 · 1 comment · Opened Jan 14, 2026
The Colab notebook Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

RosettaCommons/RFdiffusion#438 · 2 comments · Opened Jan 9, 2026
Numpy problem when running with Docker Open

RosettaCommons/RFdiffusion#435 · 3 comments · 1 assignee · Opened Dec 12, 2025
The cyclic peptides generated by RFdiffusion are not closed. Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

RosettaCommons/RFdiffusion#434 · 1 comment · Opened Dec 8, 2025
Error: Multiple chain IDs in chain: {'A', 'B'} Open

RosettaCommons/RFdiffusion#432 · 3 reactions · 1 assignee · Opened Dec 6, 2025
Primary config directory not found. Open

RosettaCommons/RFdiffusion#431 · 6 comments · 1 assignee · Opened Dec 3, 2025
With symmetry, Hydra throws minor warning Open

Difficulty 1/5 Under an hour Newbie friendliness 55/100

RosettaCommons/RFdiffusion#427 · Opened Nov 23, 2025
Seeking guidance on hotspot specification and unexpected results Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/RFdiffusion#423 · 2 comments · Opened Nov 18, 2025
outdated requirements, how to install on cuda 12.x and python 3.11 or later ? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

RosettaCommons/RFdiffusion#422 · 1 comment · 1 reaction · Opened Nov 17, 2025
Installation support for Windows / WSL users (CUDA, DGL, cu117 issues) Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#421 · 1 comment · Opened Nov 13, 2025
How to generate multiple helices instead of one long helix when extending a protein backbone with RFdiffusion？ Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

RosettaCommons/RFdiffusion#414 · 3 comments · Opened Oct 23, 2025
AME Benchmark Clarification Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

RosettaCommons/RFdiffusion#412 · 2 comments · Opened Oct 18, 2025
Cannot install RFDiffusion on VM with X86-64, pytorch_cuda-12.8.1, RTX 5090 GPU Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

RosettaCommons/RFdiffusion#411 · 4 comments · Opened Oct 17, 2025
AttributeError: 'SelfConditioning' object has no attribute 'idx_pdb' Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

RosettaCommons/RFdiffusion#408 · 2 comments · Opened Sep 28, 2025
Cyclic peptide design issues Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#406 · 2 comments · Opened Sep 27, 2025
Question: RFpeptides Branch - Should I clone the branch directly or merge with main for containerization? Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/RFdiffusion#405 · 3 comments · Opened Sep 26, 2025
Missing sidechain of target in output Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#403 · 6 comments · Opened Sep 23, 2025
Cyclic peptide structure prediction Open

Difficulty 1/5 Under an hour Newbie friendliness 25/100

RosettaCommons/RFdiffusion#401 · 1 comment · Opened Sep 16, 2025
No cyclic backbones are generated with RFpeptide! Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

RosettaCommons/RFdiffusion#400 · 4 comments · Opened Sep 16, 2025
Succes rate Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/RFdiffusion#399 · 5 comments · Opened Sep 11, 2025
Cannot install RFDiffusion on aarch 64, Ubuntu 22.04, CUDA 12.8 (GH200 GPUs) Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#398 · 8 comments · Opened Sep 7, 2025
different protein samples Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

RosettaCommons/RFdiffusion#397 · Opened Sep 4, 2025
Is it possible to design Symmetric Oligomers binding to target protein Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

RosettaCommons/RFdiffusion#396 · 2 comments · Opened Aug 29, 2025
RFdiffusion Colab Setup Cell Not Working: ModuleNotFoundError: torchdata.datapipes Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

RosettaCommons/RFdiffusion#394 · 1 comment · Opened Aug 22, 2025
No module named 'yaml' Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

RosettaCommons/RFdiffusion#393 · Opened Aug 21, 2025
Decreasing Success Rate in Binder Design Across Repeated, Independent Runs with Identical Parameters Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#391 · 4 comments · Opened Aug 21, 2025
Question: Exploring the Optimal Range for Denoising Timesteps (Iterations) in Binder Design Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/RFdiffusion#389 · 4 comments · Opened Aug 18, 2025
partial diffusion with an antibody-antigen complex structure Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

RosettaCommons/RFdiffusion#388 · 1 comment · Opened Aug 17, 2025
Example of Improved Protein Binder Design Using Beta-Pairing Targeted RFdiffusion Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/RFdiffusion#385 · 1 reaction · Opened Aug 12, 2025
RuntimeError: mat1 and mat2 shapes cannot be multiplied (192721x92 and 103x64) Open

Difficulty 4/5 3-5 days Newbie friendliness 10/100

RosettaCommons/RFdiffusion#384 · 1 comment · Opened Aug 6, 2025
Problem while installing LigandMPNN Open

Difficulty 3/5 1-2 days Newbie friendliness 20/100

RosettaCommons/RFdiffusion#383 · 2 comments · Opened Aug 5, 2025
RFPpeptides protocol Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#375 · 12 comments · Opened Jul 24, 2025
Inquiry Regarding Running RFdiffusion Colab Notebook (diffusion.ipynb) on ARM64 Architecture (Jupyter Notebook Attempt Failed) Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

RosettaCommons/RFdiffusion#374 · 6 comments · Opened Jul 23, 2025
[Bug] ModuleNotFoundError: No module named 'torchdata.datapipes' on Linux aarch64 (DGL incompatibility) Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

RosettaCommons/RFdiffusion#373 · 2 comments · Opened Jul 22, 2025
RuntimeError: PytorchStreamReader failed reading zip archive: failed finding central directory Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

RosettaCommons/RFdiffusion#372 · Opened Jul 19, 2025
why cyclic peptide doesnt work for chain b Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#371 · 1 comment · Opened Jul 18, 2025
RuntimeError: CUDA error: CUBLAS_STATUS_NOT_INITIALIZED when calling `cublasCreate(handle)` Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#369 · 2 comments · Opened Jul 17, 2025
Possible error in receptor_con_hal_idx0 variable in trb file Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

RosettaCommons/RFdiffusion#368 · 1 reaction · Opened Jul 16, 2025
Picking Hotspot Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#367 · 1 comment · Opened Jul 16, 2025
Question on intended bin definitions for L2D Loss in RFDiffusion Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

RosettaCommons/RFdiffusion#366 · Opened Jul 15, 2025
Design cyclic peptides with disulfide cyclization Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

RosettaCommons/RFdiffusion#364 · 1 comment · Opened Jul 10, 2025
Issue with Cyclic Peptide Generation Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

RosettaCommons/RFdiffusion#363 · 11 comments · Opened Jul 10, 2025
Incorrect output pdb format after binder design on Colab notebook Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

RosettaCommons/RFdiffusion#362 · 4 comments · Opened Jul 8, 2025

RosettaCommons/RFdiffusion

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