dMaSIF
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FreyrS
Hi, I wanted to ask whether modeled ligands or PTMs (e.g. phosphorylated residues) that are in the same chain as the polypeptide are included in the descriptor calculation?
Hi, I found a link to Huggingface with pre-trained weights. It seems to be NOT up now. Is there a pre-trained model that this paper have on Hugging face. Thanks...
Dear Authors, Thank you for sharing the work and code! I have some problems regarding the AUC-ROC and loss function part. In > https://github.com/FreyrS/dMaSIF/blob/0dcc26c3c218a39d5fe26beb2e788b95fb028896/data_iteration.py#L202-L215 You seemed to sample a random...
Hi there, I'd like to know is it feasible to train dMaSIF model without download the masif_site_masif_search_pdbs_and_ply_files.tar.gz file, and using dMaSIF data_preprocessing code only.
Hi Thanks for making your code public. I want to run main_inference.py for site prediction. The only pretrained model you provide is this one for search prediction dMaSIF_search_3layer_12A_16dim when I...
Dear Authors, This is really an amazing body of work, thank you. Would you have any suggestions as to how to adapt dMaSIF for tasks where we want to predict...
python main_inference.py --experiment_name dMaSIF_site_3layer_16dims_9A_0.7res_150sup_epoch85 --embedding_layer dMaSIF --emb_dims 16 --n_layers 3 --resolution 0.7 --radius 9 --single_pdb 1A0G_B_B --site True --device cuda:0 0%| | 0/1 [00:00
How can I get .ply corresponding to .pdb as provided in download dataset? In other words, how does this work convert pdb to ply?
Dear dMaSIF team and users, I am using the Google Colab version of dMaSIF to get the surface predictions from the model protein pdb files. Among the outputs of dMaSIF...
