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durrantlab / wisp

WISP is a trajectory analysis tool that calculates and visualizes allosteric pathways.
https://durrantlab.github.io/wisp/
Academic Free License v3.0
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Cutoff distance #6

Open daviddelima opened 2 weeks ago

daviddelima commented 2 weeks ago

Hi, I was reading the documentation and the publication, and I didn't see the cutoff distance used to define if two adjacent residues are allosteric.

jacobdurrant commented 1 week ago

Hi @daviddelima,

Much thanks for your interest in WISP. WISP doesn't use a cutoff distance between the orthosteric and allosteric sites. It calculates the path between adjacent residues that might connect these sites. That said, in terms of practical use, if the orthosteric and allosteric sites are very far away, the program often gets stuck in a combinatorial explosion and ends up taking a very long time to run. So it's good to not pick orthosteric and allosteric sites that aren't too distant. I hope this answer helps.

All the best, Jacob

daviddelima commented 1 day ago

Hi, Jacob!!! I was able to run this command --source_residues A_PLP_645 --sink_residues E_PLP_1449 from a 33G PDB ensemble. It didn't work on my computer but it work in the cluster, I used many cores for memory purposes.

These two residues are 70 A apart and the calculations took 90 minutes; however, when I visualized the path, it terminated around 40 A from the source residues going to the direction of the sink residues at residue Term (placer name for where the path terminated because algorithm issues). Let's call this path, path B - from source residue to residue Term.

Now, is it computationally correct if I started a secondary WISP calculation from residue Term as the source residue to the sink residue (path B)? And then, when I visualize it, I will connect path A and B?