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Hello, thanks for the awesome package! It is of great help for my project :)
I am using the 'flood_fill_above' function to search for blobs in specific locations of the Fo-Fc map.
While testing my…
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`Processing BRD4: complex 1 of 1`
`Trying to load data/predict/BRD4/BRD4_ligand.sdf`
`Docking the receptor data/predict/BRD4/BRD4_protein.pdb`
`To the ligand data/predict/BRD4/BRD4_ligand.sdf`
`Tr…
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Hi Cédric,
I've been encountering an issue when creating a prolif molecule from a PDB file. I run
`
u = mda.Universe(filename)
prolif.Molecule.from_mda(u)
`
And the debug shows the error arise…
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**Description**
I'm trying to find parameters for Zinc Ligand.
But the problem is one of the step is to use rdkit MMFF94s filed to find charges, that field doesn't have Zn in it's atom types so it f…
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Currently, matching for scoring (and for setting up transformations) is done entirely based on MCSS search. In some cases this will be undesirable, such as when a ligand binding mode is expected to be…
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Hello,
I can't find information regarding the Autodock-GPU batched ligand pipeline.
Are there example scripts available to summarize and sort the results of batch docking? Or generate the -filel…
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When I attempted to train the code with train.py and the provided simple example it2_tt_0_lowrmsd_valid_mols_test0_1000.types and crossdock folder, the model froze in the dataloader next_batch part.
…
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### Model Title
Tox21 NR-AR-LBD
### Publication
Hello @Yayeks!
As part of your Outreachy contribution, we have assigned you the dataset "Tox21 NR-AR-LBD" from the Therapeutics Data Commons to tr…
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https://mp.weixin.qq.com/s/boDawuFSHqY_LuXLyPOYsg
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Dear Developers,
Thanks for providing fantastic work on the funnel metadynamics pipeline.
Here is a question about funnel correction term since the [paper](https://www.pnas.org/doi/10.1073/pnas.…