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Support for different protein conformations in the protocol would be desirable for some of our users. for the Non Equilibrium Cycling or Switching this can be done just by allowing different protein c…
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For molecules with saturated ring systems (e.g. sugars) it can be useful to implement sampling of initial ring conformations, dock them separately and choose best output. This looks critically importa…
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I found that 'root_3_xyz' has been used directly when converting vBAT back to Cartesian coordinates. Do the 'root_3_xyz's same as heavy atoms in residues? Does it mean the heavy atoms are fixed in rec…
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Hi Zach,
I'm trying to install the latest commit, b2add37. Five of the nosetests fail. Here's a few lines from the output:
```
EEEE......E
=====================================================…
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```
In this work, we aim to aid the training of Hamiltonian-predicting models and NNPs for druglike
molecules by significantly extending and improving the nablaDFT dataset [11]. We double the number…
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Currently, the repack function uses the SpinLabel.sample() method to sample new label conformations. This method always samples from the underlying rotamer library and not the current state of Rotamer…
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Hi developers:
I have a molecule with this SMILES: ```CO[C@@H]1C[C@@H](CN(C)C(=O)c2csc([SH](N)(=O)N3CCCCC3)c2)[N@@H+](C)C1```
It looks like
![1635915671(1)](https://user-images.githubusercontent.…
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Hello, I am starting a new project with code your uploaded. But confusingly, when I downloaded and installed the biobox, errors are reported. With a few days of trying, I found the version of biobox i…
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I'm going over ligands to choose something to demonstrate BespokeFit's symmetry cleverness, and I noticed that `data/shp2/02_ligands/ligands.sdf` has some suspect structures, such as `lig_E23`, (state…
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I would like to know how the train.lmdb and valid.lmdb files in the docking_v2/protein_ligand_binding_pose_prediction_v2 directory were processed from the MOAD dataset. I have checked the code and fou…