Owner

RosettaCommons

10 indexed repositories · View on GitHub

RFdiffusion
Code for running RFdiffusion

Python · 3052 stars
foundry
Central repository for biomolecular foundation models with shared trainers and pipeline components

Python · 966 stars
PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

Jupyter Notebook · 709 stars
rosetta
The Rosetta Bio-macromolecule modeling package. Available through license with the University of Washington.

C++ · 470 stars
atomworks
A generalized computational framework for biomolecular modeling.

Python · 446 stars
RFdiffusion2
Inference code for RFdiffusion2

Python · 443 stars
binder
Binder, tool for automatic generation of Python bindings

C++ · 369 stars
RFDpoly
A diffusion-based ML model for de novo design of DNA, RNA, proteins, and mixed assemblies.

Python · 29 stars
documentation
Documentation for Rosetta Applications. The source for the Rosetta documentation wiki.

PostScript · 10 stars
tools
Tools for parsing Rosetta source code and scripts for running specific Rosetta applications.

Python · 9 stars

Beginner friendly Everything

Open All

RF3 training cutoff uses PDB deposition date — implications for temporal benchmark leakage Open

RosettaCommons/foundry#381 · 2 assignees · Opened Sep 18, 2026
[Bug] RF3 validation step in end-to-end notebook uses undesigned RFD3 backbone instead of MPNN-designed structure, causing abnormally high RMSD Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

RosettaCommons/foundry#380 · Opened Sep 10, 2026
Dependency on biotite 1.4.0 requires pdbx_PDB_ins_code in atom_site type cifs Open

RosettaCommons/atomworks#99 · 1 assignee · Opened Aug 19, 2026
[BUG] Hydrogen Bond Metrics Not Getting Calculated Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 76/100

RosettaCommons/foundry#374 · Opened Aug 14, 2026
[BUG] RFdiffusion3 not respecting positions of fixed atoms in unindexed residues Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

RosettaCommons/foundry#372 · 1 comment · Opened Aug 12, 2026
Stale .ccd_codes_cache: components added under an existing letter dir are silently invisible Open

Difficulty 3/5 1-2 days Newbie friendliness 64/100

RosettaCommons/atomworks#97 · Opened Aug 11, 2026
sheet_fraction and helix_fraction Open

question

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

RosettaCommons/foundry#370 · 2 comments · Opened Jul 30, 2026
[QUEST] Inpainting residues with RFD3 only gives glycines Open

question

Difficulty 5/5 Over a week Newbie friendliness 35/100

RosettaCommons/foundry#366 · 4 comments · Opened Jul 22, 2026
atomworks should ignore obsoleted CCD codes Open

RosettaCommons/atomworks#94 · 1 assignee · Opened Jul 20, 2026
[BUG] RFD3 might have problems in reading PDB format file with HETATM inside. Open

bug RFdiffusion3

RosettaCommons/foundry#365 · 1 comment · 1 assignee · Opened Jul 16, 2026
Repeated RosettaDock crashes Open

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

RosettaCommons/rosetta#739 · 1 comment · Opened Jul 16, 2026
[Bug]`int()` parsing failure when component contains `P` suffix during RFD3 input parsing Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

RosettaCommons/foundry#362 · Opened Jul 8, 2026
Problem with lowres docking script hanging after a couple of decoys Open

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

RosettaCommons/PyRosetta.notebooks#116 · 1 comment · Opened Jul 2, 2026
[QUEST]multiple GPUs Open

question

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

RosettaCommons/foundry#336 · 6 comments · Opened Jun 30, 2026
[BUG] Denoised and noisy trajectories are accidentally swapped during reshaping in inference engine Open

RosettaCommons/foundry#335 · 1 assignee · Opened Jun 29, 2026
FastRelax on RoseTTaFold3 protein-ligand complexes Open

RosettaCommons/rosetta#721 · 2 comments · 1 assignee · Opened Jun 24, 2026
[BUG] RFD3 unindexed motif loss uses an atom-level mask as a token-level mask Open

bug

RosettaCommons/foundry#330 · 2 assignees · Opened Jun 22, 2026
sugar chains Open

question

Difficulty 5/5 Over a week Newbie friendliness 30/100

RosettaCommons/foundry#328 · 2 comments · Opened Jun 21, 2026
Designing a symmetric binder Open

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

RosettaCommons/RFdiffusion#456 · 3 comments · Opened Jun 8, 2026
[QUEST] Open

question

Difficulty 5/5 Over a week Newbie friendliness 35/100

RosettaCommons/foundry#291 · 3 comments · Opened Jun 2, 2026
Strategies for retaining the hydrogen-bond donor/acceptor architecture defined in the RFD3 active-site model during LigandMPNN sequence optimization Open

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

RosettaCommons/foundry#289 · 1 comment · Opened Jun 2, 2026
How to generate cyclic backbone with rfdiffusion2 Open

RosettaCommons/RFdiffusion2#49 · 2 comments · Opened May 27, 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
Ambiguous inter-chain attention indices definition Open

RosettaCommons/foundry#280 · 1 assignee · Opened May 16, 2026
[BUG] RFD3 symmetry fails for odd dihedral groups D3/D5 Open

bug

RosettaCommons/foundry#278 · 1 assignee · Opened May 13, 2026
[BUG] RFD3 is missing training data artifacts Open

bug

RosettaCommons/foundry#276 · 1 assignee · Opened May 8, 2026
Diffusion of unindexed fixed residues islands with unindexed unfixed island Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

RosettaCommons/foundry#274 · 3 comments · Opened May 4, 2026
Missing ligand at zero occupancy Open

bug

RosettaCommons/foundry#271 · 1 assignee · Opened Apr 20, 2026
[BUG] Open

bug

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

RosettaCommons/foundry#266 · Opened Apr 7, 2026
Formal charge correction fails in the presence of bonds to metal ions Open

RosettaCommons/atomworks#80 · 1 comment · 2 assignees · Opened Apr 7, 2026
RF diffusion colab- RMSD Open

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

RosettaCommons/RFdiffusion#449 · Opened Apr 3, 2026
Subject: Help with restricting protein binder design to specific RNA loop region Open

RosettaCommons/RFDpoly#7 · 1 assignee · Opened Apr 1, 2026
[QUEST] Glycans as target Open

question

RosettaCommons/foundry#255 · 1 comment · 1 assignee · Opened Mar 31, 2026
[BUG] Unphysical sidechain rotamers generated for His, Lys, and more Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

RosettaCommons/foundry#251 · 1 comment · Opened Mar 25, 2026
Readme contains CLI commands for a version >v0.1.10 Open

Difficulty 2/5 1-3 hours Newbie friendliness 57/100

RosettaCommons/foundry#249 · Opened Mar 24, 2026
Partial diffusion returning the input molecule without modifications Open

question

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

RosettaCommons/foundry#247 · 2 comments · Opened Mar 23, 2026
[QUEST] Fixing one chain for redesign with RFD3 + LigandMPNN Open

question

Difficulty 4/5 3-5 days Newbie friendliness 42/100

RosettaCommons/foundry#246 · Opened Mar 23, 2026
5070Ti cuda error Open

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

RosettaCommons/RFdiffusion#444 · 6 comments · Opened Mar 17, 2026
Metadata generation Open

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

RosettaCommons/atomworks#79 · Opened Mar 15, 2026
[BUG] Residue and/or chain IDs not matching when using select_fixed_atoms constraint Open

bug

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

RosettaCommons/foundry#241 · Opened Mar 12, 2026
[BUG] Runtime TRITON error with RF3 on Collab T4 GPU Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

RosettaCommons/foundry#240 · 1 comment · Opened Mar 12, 2026
Do I need to setup CCD and PDB PATH mirrors, if I just want to prepare .cdf and .sdf files from .pdb for use in RF3? Open

question

RosettaCommons/atomworks#78 · 5 comments · 1 assignee · Opened Mar 9, 2026
Pure CPU computation? Open

enhancement

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

RosettaCommons/foundry#237 · Opened Mar 9, 2026
Lost string annotations because of array monkey patch Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

RosettaCommons/atomworks#77 · 1 comment · Opened Mar 6, 2026
Deformation of coordinate space Open

question

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

RosettaCommons/RFdiffusion#443 · Opened Feb 24, 2026
Running RFD3 - network_input (X_noisy_L) for example_id ? Open

question RFdiffusion3

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

RosettaCommons/foundry#225 · 5 comments · Opened Feb 23, 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
Question: Variable usage in RF3 Validation block (mpnn_outputs vs atom_array)? Open

question

RosettaCommons/foundry#224 · 1 comment · 1 assignee · Opened Feb 19, 2026
Virtual atoms remain superimposed on C-alpha Open

bug RFdiffusion3

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

RosettaCommons/foundry#217 · 1 comment · Opened Feb 17, 2026
RF3 error ConvertTritonGPUToLLVM Open

bug

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

RosettaCommons/foundry#214 · 5 comments · Opened Feb 16, 2026

Showing the newest 100

This page lists what was indexed most recently. Advanced filter has the whole inventory, narrowed by language, difficulty and how long a task takes.

Open advanced filter

RosettaCommons

Showing the newest 100

Get new issues in your inbox