DiffSBDD
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arneschneuing
A Euclidean diffusion model for structure-based drug design.
Dear, @arneschneuing I am currently working on structured-based drug design (SBDD) and have been deeply impressed by your remarkable performance of your molecule generation work. Also, Thank you for sharing...
Hello, I have been following the work of DiffSBDD for several months. It is truly a creative work. However, I found the paper in arxiv was updated and the latest...
* Now overriding global `dataset_info` properties when processing CrossDock using only Ca atoms, as otherwise these values would not be updated (i.e., correct) e.g., for `amino_acid_dict` at runtime. * To...
Hi, I am trying to set DiffSBDD cond method as one of baselines in my work, I would like to sample mols given 100 pockets from the test set of...
Hi Arne, thanks for this excellent work. I plan to replace Autogrow with your model in one of my SBDD pipelines. However, in the module constants.py, I found that, for...
I would like to use the DDIM version of your conditional ddpm version as a baseline in our work. Since our method, which is not a diffusion model, supports fast...
Hi, When I try to run generate_ligands.py, I get the following error: **_Segmentation fault (core dumped)_** I am running on an NVIDIA RTX A4500 GPU, with 20470MiB VRAM, and I...
Hello, thank you for your previous question. Unfortunately, I was not able to fully replicate the process, but I used the same calculation method to evaluate the ligands generated by...
When I run > (sbdd-env) user@machine:~/projects/repos/DiffSBDD$ python generate_ligands.py ./checkpoints/full_atom.ckpt --pdbfile ./data/targets/test_1.pdb --outdir ./outputs/test_1/ --resi_list A:115 A:121 A:123 I get the following error: > OSError: /home/user/miniconda3/envs/sbdd-env/lib/python3.10/site-packages/torch_scatter/_version_cuda.so: undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKSs This error...
Thank you for the great works! I wondering why you used different loss_t for training and validation or Is there any problem to use the same method to calculate the...
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A Euclidean diffusion model for structure-based drug design.