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Hi,
In the paper, SIGN was tested on the PDBBind 2016 and CSAR, but I can't find any codes related to CSAR in the respository. Can you provide a script or any other methods to evaluate SIGN on CSAR…
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Hi,
I am experimenting a problem with a ligand downloaded from Zinc15 that have been converted to pdbqt.
The problem is the following:
$ vina-gpu+ --config ./docking_conf_1.txt
#############…
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After reading your documentation I didn't find a script that will tell the docking software to bind a ligand in a specific area/residues desired. Can you help me in that?
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https://doi.org/10.1101/099358 (http://biorxiv.org/content/early/2017/01/10/099358)
> Many biological processes are governed by protein-ligand interactions. Of such is the recognition of self and n…
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Hi,
I have used vina-gpu with some ligands.
In the config file I have used the lines:
num_modes = 5
log = vina-gpu2_docking_res_small_sample_size.log
The first lines of the log file are the f…
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Our partners at the Univ. Kansas have successfully produced Pf CLK1 and PKA-R in milligram quantities for ligand binding and structural studies. We previously predicted these two proteins as the most …
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I would like to calculate the dG of a ligand binding to a protein via the LIE method:
dG = alpha(Uvdw(bound) - Uvdw(free)) + beta(Uelec(bound) - Uelec(free)) + gamma
It appears that some special s…
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**What is this request referring to?**
Constitutively activating variant
**What is the name you would like SO to give the term?**
constitutively_activating_variant
**What is the definition tha…
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Contrary to the AlphaFold3 server, we now can include water molecules as ligands. Using ccdCodes works really well (and probably water smiles work too, but I have not tried) :
`"ccdCodes": ["HOH"]`…
smg3d updated
2 weeks ago
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@ConorFWild says that combi-soaks are handled already in XCA and have been tested with Jasmin's dataset (private DENV target on staging) but @tdudgeon says that the CIF parsing in the collator and ali…