Paul Francoeur

The data we utilized is downloaded directly from the PDB at the time of the data creation, we only took the affinity numbers from the PDBbind data and were matching...

Or did I misunderstand, and you meant exactly the PDBbind2016 data?

Additionally, looking at the 5c28 example you mentioned, the molecules are the same. Could you provide more examples of faulty data, and also describe how you are trying to re-compute...

For the RMSDs that we reported, we used obrms to calculate them (comes when you install openbabel).

Bug from file generation would be my guess. By definition they should all be 1 and non-negative

I uploaded a fixed version of the types file. I also re-ran the training of the Default 2018 model on the PDBbind crystal data, test on the core set. Paper...

The model file is unchanged (it only describes the network setup, which is just the default2018 architecture), and when training you generate your own weights files. This setup of train...

Dense net caffe model architecture does not have a RMSD column, the def2018 architecture does. You need to use different types files for the Dense net, which I suspect is...