Hydrogen bond importance sliders?

Started by BootsMcGraw

BootsMcGraw Lv 1

We now have "new sliders for sidechain and backbone hydrogen bond importance".

What do these do, other than reduce my score? Can someone please explain how they work, and when/why we would use them? The Wiki has little to say about them.

joshmiller Staff Lv 1

Hi Boots,

Great questions, sorry for the lack of clarity when releasing this feature.

The new behavior options are simply there to be additional tools for you. Similar to clashing importance, you might find that lowering or raising a subscore's importance may help you get into a better fold. I think some of our scientists said that the hbond subscore importances might be helpful for forming hbond networks or making bonds with a binder target. Ultimately, this is just more power for you to shape the protein as you'd like!

In terms of what tools to use them with, they work exactly like Clashing Importance, so they should affect whichever tools CI affects.

Technically speaking, what all of these sliders do is change the score function used by tools, making tools believe they are making an improvement by weighting the importance of certain subscores differently. However, the Score displayed at the top always uses the unmodified score function, so you will never get an increased score directly by modifying slider values.

So far in my experience, the best way to use them is to crank them up when trying to form hbonds, then you can bring them back down to 1 when your hbonds have formed. The backbone hbond slider might also be useful as a slider for how much you care about your secondary structures keeping all of their backbone-backbone bonds. And the sidechain slider is probably useful when trying to make more bonds to a target for binder puzzles.

Hope this helps! Good luck with experimenting with them and let us know what you find!

BootsMcGraw Lv 1

There are many subscores used when calculating the total score.

Which subscores are modified by each slider?

I assume that increasing the slider value above one more heavily weights that/those subscore(s) relevant to the unmodified subscore values, and decreasing the slide value below one less heavily weights that/those subscore(s) relevant to the unmodified subscore values.

Formula350 Lv 1

It's only the "Bonding" subscore. We, as players, cannot see how the subscores are broken up into, as we're given the "dumbed-down" version.

Unfortunately this means that BOTH modify the Bonding subscore, but that both impact it differently. Sidechain slider impacting only Sidechain-to-Sidechain and Sidechain-to-Backbone bonds, and Backbone slider only impacting Backbone-to-Backbone bonds.
But yes, the weights work as you said. The end result, though, works in the opposite way that Clashing does. Where Clashing will compact your protein the lower your make it, these HBond sliders will have the tendency to compact it the higher you make them. As bonds that might be weak, will in turn get stronger by bringing stuff closer together.

Sorry about the Wiki not having this info yet, I'm still working on the page. (It'll be at this page when it's done: https://foldit.fandom.com/wiki/Behavior_Menu)

ichwilldiesennamen Lv 1

I agree that more experimenting with these sliders/LUA functions is required. With your explanation and the wiki I understand now what they are meant to be used for and I am motivated to try them out. Thank you all! But in addition to this, I would appreciate a function in LUA to detect if a HBond has actually formed. Or in general, if a sidechain has HBond or not or how many. Maybe this can be used to automate the creation of HBonds and improve solution quality in conjunction with the slider-functions. This feature was requested by jeff101 some time ago and I think this is a very good idea! I do not see that there is a function to reliably (or at all) do this at the moment.

jeff101 Lv 1

<pre>In ED Puzzles, I have often wanted to fold the protein away from the influence of the ED cloud. Would it be possible to make a slider that controls the importance of the density subscore, ignoring this subscore when set to 0 and giving this subscore full weight when set to 1? Then, when this slider is set to 0, our protein will behave like it is folding outside the influence of the ED cloud.

Having such a slider might help if after folding
a while with the slider set to 1, some part of
our protein seems stuck in a bad place because
it happens to have a good density subscore there.
We could then switch the slider to 0 until this
part of our protein moves to a new location,
and then reset the slider to 1 to improve how
the protein fits into the new location in the
ED cloud.</pre></code>

jeff101 Lv 1

Right now, a Foldit client I am using has sliders
in the Behavior Menu for 3 different things:
Clashing Importance, Sidechain H-Bonds, and
Backbone H-Bonds. It would be nice if one could
add to this menu a slider for Density Importance.

I think there are LUA handles for the above 
sliders as well as ones for other subscores.
These LUA handles should let Recipes control
the settings of the different sliders, even
ones that the Foldit GUI does not show.

Perhaps one could add to the Behavior Menu a 
submenu with checkboxes for different subscores.
It would then add a slider to the Behavior 
Menu for every subscore checked in the submenu.
This would let us customize which things we
wanted to monitor or control manually.

kumarkuldeep6 Lv 1

I assume that increasing the slider value above one more heavily weights that/those subscore(s) relevant to the unmodified subscore values, and decreasing the slide value below one less heavily weights that/those subscore(s) relevant to the unmodified subscore values.