u/Sea-Collection-8844

Hi everyone,

I have been tasked with finding suitable positive and negative controls for lysozyme docking, and I wanted to ask how others would approach this.

At the moment, my plan for positive controls is to search the PDB for co-crystallised lysozyme–ligand complexes, then use known lysozyme binders from those structures as reference ligands. My understanding is that these could be useful for validating the docking workflow by checking whether the known binder docks into the correct pocket, reproduces a reasonable pose, and gives a sensible docking score.

One thing I am unsure about is how much attention I should pay to the protein sequence when selecting the positive control. For example, should I check whether the lysozyme structure contains mutations before choosing it as a reference? Or is that something you would only investigate later if the positive control fails to dock well?

For negative controls, I have seen people recommend using DUD-E decoys or similar property-matched decoys. Is that generally the standard approach for this kind of docking validation, or are there better options for lysozyme specifically?

I am also wondering whether it would make sense to design a Markush-style representation based on known lysozyme binders, such as sugar-like or N-acetylglucosamine-like scaffolds, and then generate/screen related compounds. I am not fully sure how practical this is, so I would be interested to know whether anyone has tried something like this.

Any advice on how to choose good positive/negative controls for lysozyme docking would be really appreciated.

Hey guys,

I have been trying to port a CPU-based docking workflow to GPU docking, as I was under the impression that GPU docking would be significantly faster than standard CPU docking.

My current setup includes one A100 GPU. From what I understand, GPU molecular docking tools such as Uni-Dock work best when you provide a batch of ligands, and the program handles the batching internally.

For comparison, I also have access to many CPU cores 432 cores in total and I am currently running 432 Vina jobs in parallel to maximise throughput.

However, I am seeing the following performance:
` GPU docking: ~15 ligands/s

CPU docking: ~100 ligands/s `

Do you think I might be doing something wrong in how I am using the GPU, or is this kind of performance difference expected depending on the docking setup, ligand batch size, and CPU parallelism?

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For those who currently live there, what has your experience been like?