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One assay is reported for all fractions. This does not allow to model fractionated design with channel swaps between fractions (though I don't know how relevant this is).
Example: consider Assay 1 (A…
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Hi,
I'm trying to virtual screening with vina's batch mode using Python API.
According to docs, `set_ligand_from_file` looks to take multiple ligand PDBQT files as arguments.
I think PDBQT f…
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Hi @olibclarke,
thank you very much for the very useful and nicely commented aliases and startup commands!
From what I tested so far they work fine except the `default_mol_display` hid the cryoE…
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# Background
The docking calculation can fail for different reasons. The docking failure for a particular ligand should not affect other ligands.
# Scope of work
* Show docking results for all …
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During the rerun step, `gmx mdrun -rerun` is used to obtain potential energies of each of the sampled conformations of the system using every hamiltonian. During this process, if the potential energy …
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I have a question regarding addmodulescore. I have prepared a list of ligands and their receptors that are of interest in a specific disease. how to laverage addmodulescore and what I can deduce from…
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To prevent from repeated work, an option to filter the input list of ligands based on output tables is desired. It should be possible to electively use this filtering, as in some cases it may be desir…
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It seems like some annotations contain upstream proteins that should be annotated to 'regulation of NF-kappaB signal transduction' and/or using the relation 'acts upstream of or within' for the NF-kap…
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Hello, I am not sure whether I should post this question here or at the BioSimSpace repository, but I am trying to understand how we can set the "forcefield" property that is required when we want to …