Make hydrophobic interactions visible

Started by Susume

Susume Lv 1

In the scientist chat on April 19 it came out that hydrophobic interactions are desirable in design puzzles, perhaps even more desirable than hydrogen bonds. The problem is, while we can see hydrogen bonds in the game, we can't see if we are making hydrophobic interactions better or worse. Would it be possible to add a coloring option to the view menu to color hydrophobic residues better or worse, based only on the portion(s) of the score that reflect hydrophobic interaction? Then we could see if we are improving the protein's ability to stick to its target. There may be some better way to implement it, but in any case, please let us see the thing you would like us to optimize.

infjamc Lv 1

Or better yet… why not generalize to coloring relative to a custom set of score function terms? I'm thinking about something like this:

[X] Color relative to the following score terms:

  • Clashing
  • Packing
  • Hiding
  • Backbone
  • Side chain
  • Hydrogen bonds

spmm Lv 1

Well there was a recently (Oct 2011) reported discovery of an equation:

The physical model to describe the hydrophobic interactions of molecules has been a mystery that has challenged scientists and engineers since the 19th century. Hydrophobic interactions are central to explaining why oil and water don't mix, how proteins are structured, and what holds biological membranes together. Chemical engineering researchers at UC Santa Barbara have developed a novel method to study these forces at the atomic level, and have for the first time defined a mathematical equation to measure a substance's hydrophobic character.

"According to the van der Waals theory, however, oil and water shouldn't separate and surfactants shouldn't form membranes, but they do. There has been no proven theory to account for these special hydrophobic interactions. Such behaviors are crucial for life as we know it to exist."

http://www.eurekalert.org/pub_releases/2011-10/uoc–nep101111.php

No idea if it works :)

(PS ifjamc that -1 was me trying to page down, apologies)

brow42 Lv 1

For custom scoring, I wrote Region Scorer: http://fold.it/portal/recipe/38634 . A coloring scheme would be great! However, our colorblind cohorts are already annoyed enough.

I've been wondering how I could make use of the compatibility index in http://fold.it/portal/recipe/28691 . Does this affect scoring in Rosetta? Could the effect be separated from hiding/packing?

Also, can a biochemist step in and say more about Trp-Trp bonding? I keep misreading that as Tyr-Try:

DrLemming: a short beta sheet stabilized by a cross-strand disulfide bond and two tryptophan/tryptophan interactions. The only problem: this motif is so tiny, it is difficult to do anything with; it needs to be larger but retain rigidity. Otherwise anything goes: beta sheets, alpha helix docking, rigid loops, you name it. We've given you 20 extra residues to play with.

Susume Lv 1

To avoid the difficulty with colors, the hydrophobic interaction between two residues could be shown as a line connecting them (similar to a hydrogen bond but with a different texture) if its strength surpasses some threshold. The thickness of the line could indicate the degree to which the interaction increases the stickiness between the residues. The lines could be turned on and off through the view menu.

beta_helix Staff Lv 1

Thank you for bringing this up, we'll try to add a visualization to the game as soon as we can!

BootsMcGraw Lv 1

As chief mouthpiece for The Colorblind Folding Contingent, I thank you in advance for considering us when making revisions to the displays of the game.