Rocco Moretti

RFdiffusion is a tool to create backbone structure. It does not attempt to determine the amino acid identity of the newly created residues. As such, it's expected that the output...

The output PDB files from RFdiffusion include the generated backbone 3D coordinates. ProteinMPNN and other such sequence design tools (typically) do not change the backbone coordinates, but they will change...

> The authors' method seems like a local "sequence-structure co-optimization," whereas my idea is more of a "fixed-backbone sampling" followed by refinement. I think this encapsulates the main difference well....

I don't know why they chose 4 cycles -- my guess is that's what they found to generally work well in practice to give decently convergent results without spending too...

If you already have a general topology you wish to maintain, then [partial diffusion](https://github.com/RosettaCommons/RFdiffusion?tab=readme-ov-file#partial-diffusion) may be what you want to do. If you're more interested in rebuilding certain areas from...

On some machines, the installation installs the CPU version of pytorch, rather than the GPU one. You can check this by doing a `conda list | grep pytorch` -- if...

I'd probably recommend just trying the reinstall first, and see if it fixes things. If not, then you can try removing before re-installing. (The reason is that removing pytorch might...

Your contig map is calling for two chains, only one of which is generated from scratch. One of length 228, created from scratch, and one which is the input PDB...

I know that LigandMPNN has an option where it can output a PDB structure, though I don't think plain ProteinMPNN has that option. Normally the approach is to take the...

From https://www.nature.com/articles/s41589-025-01929-w#Sec7 > Macrocyclic peptide monomers and binders were designed with RFpeptides using a three-stage pipeline: backbone generation using RFdiffusion with the cyclic offset applied to the peptide chains, followed...