Hypersphere
Hypersphere
It would be great if you could add the capability of using complex numbers in uncertainties. This is available in the Julia package, Measurements, but I would prefer to have...
1. I have furnished the AMDock (linux) program with a modified dat file that contains parameters for Ruthenium (Ru) as follows: atom_par Ru 4.04 0.010 34.5257 -0.00110 0.0 0.0 2...
When trying to run diffdock to predict 24 protein-ligand complexes, I get the following error related to "complex_name": (diffdock) rjrich@rjr-sd1:~/DiffDock$ python -m inference --config default_inference_args.yaml --protein_ligand_csv DjCES/DjCES_dd.csv --out_dir DjCES/results /home/rjrich/anaconda3/envs/diffdock/lib/python3.9/site-packages/Bio/pairwise2.py:278:...
1. Which inference arguments can have a positive influence on prediction accuracy or confidence? For example, what is the effect of increasing the actual-steps, and/or inference_steps, and/or samples_per_complex? 2. If...
When I predict the structures of protein-ligand complexes using Boltz, the chirality of the input ligands is not being preserved. Some of the ligands have a chiral phosphorus atom and...
Getting out of memory errors with Boltz-1 version 0.3.2 when predicting protein with ~2300 residues. My GPU has 48GB memory; my CPU RAM is 256GB. I tried downloading a fresh...
Should the affinity of a small-molecule ligand for a protein receptor or enzyme be interpreted only in a relative sense or is it possible to compare the affinity predicted by...
FYI, when installing boltz-2 in a new conda environment, I encountered the following deprecation warnings: DEPRECATION: Building 'modelcif' using the legacy setup.py bdist_wheel mechanism, which will be removed in a...
Which converter(s) do you recommend for generating SMILES strings that contain correct stereochemical information from 3D ligand files in SDF, MOL2, or PDB ligand files? I have some difficult ligand...
In the affinity.yaml file in the examples folder, what does the "version number" in the first line refer to? Is this the version of boltz to use (boltz1 vs boltz2)?...