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Hi! This is a great package with many useful resources!
After looking into it, we were wondering if it can also be used to model cellular communication. More precisely, we would like to extend INDRA…
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Hi there,
We are trying to validate ABFE calculations by using Yank. We are interested to simulate a particular series of Thrombin inhibitors. The series is composed of weak binders however, the YA…
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It seems there are various cases where we have a GO synonym derived from PR, but not equivalence axiom in GO. Many of these are candidates for missing logical defs, see attachment.
Columns:
- scope
-…
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I am calculating binding free energy of Protein ligand complex, 41 lambdas. i got this error.
Traceback (most recent call last):
File "/share/anaconda2/bin/alchemical_analysis.py", line 4, in
*…
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Hi,
I am a doctoral student in China with a biomedical background. I have found your outstanding work in the drug screening work. I have encountered some problems in the installation and operation of…
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Hello, may I ask if it's possible to ensure the interaction of certain key amino acid residues during the docking process?
In fact, we need to dock a series of analogs to further determine which c…
TVect updated
9 months ago
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Mat says: Meeting link is https://ucl.zoom.us/j/99880132263 I think?
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Hi,
It seems that the code here can only evaluate the model on PDBBind. How can I use the code to predict the binding affinity of a new complex not in PDBBind? If you can provide a script or any ot…
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Hi @diogomart,
I'm trying to optimize Vina parameters to get better agreement with experiment for docked binding energies of small molecules to cyclodextrins. To do this, I'd like to be able to tak…
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Here is the docking setup and report:
GPU: RTX3090
CUDA Version: 11.7
Driver Version: 515.57
receptor = protein.pdbqt
gpu_batch = lig765.pdbqt
out = lig765_result.pdbqt
center_x = 87.603
cen…