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Mon, 07/27/2020 - 02:54
#2
1/r vs 1/r^2
Mon, 07/27/2020 - 19:51
#3
Thanks!
Thanks Jeff, I did not know that.
Tue, 07/28/2020 - 00:14
#4
1/r vs 1/r^2
Mon, 07/27/2020 - 20:04
#5
Storing greatest contributors, and charges assigned to sidechain
I notice the recipe attempts to keep track of the top three pairs contributing to repulsion, and the top three pairs contributing to attraction. When a new pair exceeds the #1 spot in these lists, it gets inserted at the top of the list and the others are pushed down. However, if a new pair falls between #1 and #2, or between #2 and #3, it is not getting added into the list as it should. The recipe is using the following values for the point charges (measured in e, elementary charge) for each amino acid:
Mon, 08/03/2020 - 22:52
#6
Thx for suggstions! There's a AA table & part charge is separate
I will try to fix the issue of when a new pair falls in between #1 & #2 or #2 & #3 in the next version of this recipe, and I will try to make the recipe more accurate by adding a band if the distance between the amino acids is below a threshold. Thank you for the suggestions! I think there is a table somewhere on how charged the various amino acids are, at http://thinkpeptides.com/aminoacidproperties.html . On the table, it seems that the isoelectric point and sidechain acidity/basicity of each amino acid can show how charged the various amino acids are. On the amino acids that have both a partial positive and a partial negative, I think the point charges should be considered separately rather than aggregated, because the partial charges do play a significant role in the binding mechanism of two proteins, as either of them can attract any charged amino acid. If they are aggregated, then those amino acids wouldn't be polar and their partial positive and negative charges wouldn't be taken into consideration. I would like to point out that in this recipe, the amino acids h, n, q, s, t, and y are assigned either 1 or -1 elementary charge depending on the corresponding amino acid pair it is compared with, as both of the polar atoms can be bonded to.
Sat, 09/19/2020 - 06:04
#7
Test
I tested it at puzzle Sadbox 1892 with Binder metrics and I find 2 times your result: Hope this helps |
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This is a really interesting idea! A couple of things you might want to consider for a future version: I notice you are dividing the charge product by the distance between charges, but Coulomb's law actually uses the square of the distance - this is important because the attractive or repulsive force decreases very rapidly with distance.
The structure.GetDistance function that foldit Lua provides gives you the distance between the alpha carbons. You might get better accuracy by locating the polar atoms themselves and adding a band between them, then asking for the length of the band. That would definitely make the recipe much slower, though. One way to limit the time increase would be to query alpha carbon distance first (which is quite fast), and only use a band to get a more accurate distance if the alpha carbon distance is below some threshold (close enough that the difference between alpha carbon distance and sidechain to sidechain distance is expected to be significant).
I hope you'll keep working on this!