Atom level enzyme active site scaffolding using RFdiffusion2

This is the official data deposition for the manuscript "Atom level enzyme active site scaffolding using RFdiffusion2" Many of the figures in manuscript were composed of analysis of large numbers of PDB files corresponding to generations of RFdiffusion2 under different conditions. These files are 100s of GB and thus we cannot store them here. To this end, we are storing them on a persistent IPD server: https://files.ipd.uw.edu/pub/ In each directory, we will either archive the source files unaltered for small files or a file that simply has the URL necessary to download the requisite files. In cases of large tar files with many PDB files, we have also included a manifest here indicating what data is expected to be present. @article{ahern2025atom, title={Atom level enzyme active site scaffolding using RFdiffusion2}, author={Ahern, Woody and Yim, Jason and Tischer, Doug and Salike, Saman and Woodbury, Seth M and Kim, Donghyo and Kalvet, Indrek and Kipnis, Yakov and Coventry, Brian and Altae-Tran, Han Raut and others}, journal={bioRxiv}, pages={2025--04}, year={2025}, publisher={Cold Spring Harbor Laboratory}}