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Recipe: nicm25.dei.TestBaseScoringCL V0
Created by Nicm25 70 133
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Name: nicm25.dei.TestBaseScoringCL V0
ID: 105209
Created on: Sat, 09/18/2021 - 15:32
Updated on: Sun, 09/26/2021 - 12:06
Description:

*demo script, test base scoring CL! (segment select,number repetition,number trimmings,number setmode,number seed,number setcount,bool fixrandom)



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Nicm25's picture
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Joined: 04/22/2020
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TestBaseScoringCL description

*note: this is demo script.

previous recipe is here
https://fold.it/portal/recipe/105164

This recipe just repeats the random mutation and quick relax to find out the base energy required for folding,
and recipe has been adjusted to run in the 'Protein Design Sandbox'.

this recipe is using one quick save slot.
and recipe will try to see whether it can relax from its current form.
and can start with bands active as constraints, even with proteins that tend to fall apart.

7 arguments
select: currently selected segment will be this argument.(they are dummies for some reason)
repetition: set number circulation for each segment. leave it at 1 if need to average them all.
range: 1-20, default: 1, function: 1 is all average, 10 is each ten segments unit
trimmings: to avoid edge effects, you can adjust number of segments to be excluded from scoring.
range: 0-20, default: 0, function: 0 is do nothing, 10 is ten segment trimming
setmode: can change restrictions on type of AA's used for mutation.
range: 1-4, default: 2, function: 1 is all including, 2 is few including Pro, 3 is not including Pro, 4 is not including Gly and Pro
seed: choose any value you like to generate random AA's by random seed.
range: 0.0-1.0, default: 0.5, function: 1.0 is plus value, 0.0 is none value
setcount: run 20 times as one set, only 0 is check mode for scoring only.
range: 0-50 (ext0-1000), default: 1, function: 1 is one set 20 counts, 0 is check mode
fixrandom: set whether to fixed random seed.
default: false, function: false is always random seed, true is fixed random seed

Nicm25's picture
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Documentation

Hi, this is an explanation of how this recipe was created....

I was trying to investigate in this recipe was true(valid) energy required for folding...
that? is that phrase you've heard somewhere before?
oops, deja vu, that was continuation here.
https://fold.it/portal/recipe/105164#comment-45132

remember that foldit uses Rosetta for fast computation in scoring.
and it may contain artifacts hence aggregated from false selectivity of lowest energy, approximate energy topography, and by not assuming thermal behavior.
we will need to think carefully when using these calculated scores in our research.

that are showing foldability of proteins as it behaves in Rosetta energy function.
of course, since we are tallying this under conditions where it is exposed to surface,
can imagine an offset 30-40 points for hydrophobic sidechains when they are on inside.

these scores (foldit base) are averaged out from about 3000 samples per sidechain,
and surrounding sidechains affect them by about 10 points.

previously, single strand was used as sheet (by foldit interface), but that is replaced by loop.
so, in Loop score is sidechains on strand are energy in fully exposed situation.

Helix score is energy that is exposed in one long helix.

Sheet score is energy of strand that is always hydrogen bonded to its neighboring strand,
except that it can't bond to proline.

*attached data
the results of loop, helix and sheet data for each sidechains.

results tabulated using this recipe are as follows.

AAIndex,loopscore,helixscore,sheetscore
A,-61.761,16.342,28.114
C,-109.153,-56.813,8.950
D,3.905,32.157,30.259
E,11.620,35.458,42.566
F,-21.687,-17.125,13.920
G,-49.748,13.591,18.561
H,-1.092,20.087,31.314
I,-53.344,-21.318,15.527
K,7.127,32.842,35.691
L,-65.907,-17.588,26.653
M,-53.065,-20.294,8.310
N,-1.932,28.864,28.470
P,27.441,-25.781,30.732
Q,6.356,28.620,36.703
R,-2.102,24.531,31.216
S,-17.461,27.712,35.788
T,-38.472,25.938,34.632
V,-77.314,-19.323,31.810
W,-50.479,-28.431,17.374
Y,-3.950,-5.916,36.762
*sigma=0.4
Nicm25's picture
User offline. Last seen 10 hours 49 min ago. Offline
Joined: 04/22/2020
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Additional experimental data (sheets loop)

we ran it for each of loop scores included in the blueprint.
each was named and tabulated based on ABEGO patterns.
however, due to few samples per segment (about 200), results may not have been accurate.

*attached data
the results of loops by Blueprint each sidechains.

results tabulated using this recipe are as follows.

BBGB:
AAIndex,samples,L1,L2,L3,L4
A,856,10.612,-29.592,-26.386,8.692
C,823,-29.825,-112.129,-112.626,-15.644
D,840,31.411,0.293,9.624,1.771
E,839,28.087,1.481,2.304,24.243
F,855,-4.756,-42.515,-33.152,-13.111
G,857,21.200,-27.523,10.549,13.463
H,795,21.220,-13.666,-0.759,19.113
I,867,-23.757,-70.228,-133.285,-18.473
K,808,25.267,-1.311,-0.412,17.730
L,848,-8.304,-69.659,-69.581,-6.994
M,821,-13.139,-66.359,-62.680,-19.605
N,840,20.312,-7.985,13.054,7.774
P,95,23.886,11.314,-23.998,-26.144
Q,891,21.891,-7.972,-4.070,20.708
R,850,19.646,-15.490,-7.600,14.341
S,818,28.263,-7.310,-1.928,19.987
T,793,31.843,-26.416,-25.122,12.317
V,861,-2.513,-73.347,-127.012,-9.042
W,834,-11.478,-65.852,-66.010,-16.633
Y,809,21.899,-24.980,-22.361,5.342
BGGB:
AAIndex,samples,L1,L2,L3,L4
A,856,4.830,-34.948,-37.691,5.367
C,823,-41.353,-119.516,-119.505,-22.211
D,840,19.230,8.022,-1.516,19.971
E,839,23.394,-2.193,-12.980,27.670
F,855,-14.987,-49.926,-47.496,-18.061
G,857,9.076,-3.875,4.849,6.164
H,795,14.700,-6.762,-15.925,15.644
I,867,-28.236,-142.417,-152.246,-18.820
K,808,18.839,-3.198,-9.861,20.477
L,848,-15.616,-79.594,-78.698,-7.288
M,821,-27.039,-68.814,-73.845,-19.528
N,840,12.494,7.598,-0.653,22.484
P,95,24.243,-2.046,-42.573,-27.801
Q,891,17.318,-6.745,-16.749,22.075
R,850,12.863,-16.062,-21.525,16.083
S,818,21.000,-7.278,-12.792,18.693
T,793,10.492,-52.929,-36.712,25.435
V,861,-15.694,-138.952,-141.766,-3.086
W,834,-28.020,-75.758,-81.737,-26.785
Y,809,7.234,-36.145,-37.083,-7.447
BEAB:
AAIndex,samples,L1,L2,L3,L4
A,856,9.351,-30.722,-40.179,13.532
C,823,-37.227,-153.343,-112.074,-13.094
D,840,35.991,3.303,-13.081,28.786
E,839,31.204,-31.219,-16.053,36.462
F,855,-7.612,-95.123,-50.988,-1.621
G,857,6.872,5.717,-35.435,12.433
H,795,25.522,-55.496,-20.509,24.029
I,867,-16.328,-136.948,-87.545,-9.725
K,808,26.950,-4.123,-22.105,33.344
L,848,-8.442,-117.205,-76.341,6.291
M,821,-24.435,-107.474,-74.620,-6.415
N,840,31.739,-0.941,-14.867,26.743
P,95,23.229,-4.542,-58.214,-31.858
Q,891,23.766,-15.777,-20.294,31.872
R,850,19.219,-57.387,-26.214,25.912
S,818,31.363,-3.948,-16.727,26.519
T,793,19.508,-48.892,-22.303,31.949
V,861,0.823,-114.833,-69.418,9.755
W,834,-26.298,-110.718,-79.049,-9.971
Y,809,10.726,-83.744,-35.825,19.759
BAGABB:
AAIndex,samples,L1,L2,L3,L4,L5,L6
A,1285,12.886,-2.513,-40.052,-43.709,17.252,28.045
C,1246,-16.722,-38.685,-97.741,-108.623,-11.368,6.463
D,1238,51.234,24.573,-4.663,-18.293,14.554,32.455
E,1253,34.073,21.574,-11.606,-13.592,28.959,43.969
F,1274,4.360,-0.979,-52.317,-55.292,-13.222,11.687
G,1276,1.468,-0.942,0.810,-37.595,24.563,16.995
H,1231,27.450,23.551,-6.607,-25.604,17.846,30.598
I,1300,5.619,-55.732,-118.703,-88.079,-16.735,12.587
K,1233,27.039,19.854,-2.586,-15.597,24.180,38.267
L,1217,18.873,-0.382,-55.048,-80.374,-10.708,28.169
M,1251,-8.611,-25.104,-70.556,-83.119,-14.845,5.989
N,1272,40.018,24.523,-3.051,-16.013,14.821,29.164
P,140,17.590,15.947,-26.256,-51.241,-21.229,27.761
Q,1297,25.004,17.174,-16.232,-22.275,23.901,37.544
R,1268,19.535,12.765,-18.130,-23.857,19.171,32.147
S,1249,30.766,21.218,-16.524,-18.566,29.397,35.120
T,1224,28.960,22.602,-27.461,-27.038,19.312,37.535
V,1265,28.555,-20.574,-120.841,-76.570,-1.540,34.240
W,1235,4.449,-8.028,-57.417,-76.329,-19.784,9.839
Y,1246,28.471,21.268,-31.547,-37.789,7.709,30.049
BBAAEB:
AAIndex,samples,L1,L2,L3,L4,L5,L6
A,1285,15.218,-8.736,-31.518,-22.486,14.594,24.346
C,1246,-20.616,-50.178,-117.062,-89.175,-9.041,-3.435
D,1238,31.955,21.745,1.831,13.548,18.165,28.258
E,1253,36.572,11.942,0.792,7.232,24.216,40.030
F,1274,-0.155,-17.612,-50.763,-32.952,-5.606,2.244
G,1276,8.306,6.221,-20.576,-19.142,27.058,14.748
H,1231,29.242,3.889,-12.245,-3.523,18.141,26.115
I,1300,2.668,-37.675,-81.749,-66.174,-19.233,10.902
K,1233,31.334,8.498,-2.181,2.779,19.334,34.844
L,1217,14.410,-27.110,-67.692,-62.837,-6.374,22.410
M,1251,-6.828,-32.877,-63.187,-58.159,-14.662,3.025
N,1272,28.874,14.302,-4.637,3.357,16.443,26.876
P,140,21.380,14.888,3.856,-38.386,-19.201,28.122
Q,1297,34.837,3.747,-12.404,-1.242,19.871,34.509
R,1268,24.797,1.010,-14.699,-7.703,13.622,27.969
S,1249,32.298,22.732,-1.393,1.727,27.783,31.547
T,1224,29.200,21.597,-28.887,-5.606,10.635,33.353
V,1265,26.401,-20.963,-84.691,-57.221,-3.320,29.967
W,1235,-1.247,-25.011,-62.508,-58.397,-14.156,5.119
Y,1246,22.579,5.275,-31.122,-14.022,16.046,22.574
BAAAGB:
AAIndex,samples,L1,L2,L3,L4,L5,L6
A,1285,23.285,-3.586,-8.198,-8.575,1.565,23.882
C,1246,-2.794,-49.282,-80.179,-42.505,-65.383,0.486
D,1238,61.190,11.320,8.604,15.363,25.676,23.167
E,1253,42.754,12.103,8.749,16.698,22.323,36.258
F,1274,24.038,-27.940,-45.553,-24.766,-36.248,0.203
G,1276,3.654,-5.932,-9.418,-9.779,27.907,16.237
H,1231,38.396,1.560,-4.697,14.302,17.940,20.642
I,1300,23.331,-41.759,-56.725,-35.054,-110.249,2.492
K,1233,35.075,8.710,8.748,13.591,21.969,30.297
L,1217,25.364,-9.167,-43.615,-28.493,-34.926,17.559
M,1251,0.187,-34.665,-49.610,-39.795,-35.772,0.849
N,1272,49.223,7.667,6.076,14.229,30.850,22.509
P,140,27.974,18.577,-34.115,-32.377,23.280,-4.894
Q,1297,36.576,5.822,5.353,7.899,28.231,29.436
R,1268,30.499,0.773,3.391,6.129,14.100,29.428
S,1249,38.779,8.365,5.415,10.953,18.378,29.785
T,1224,35.406,3.353,-4.911,10.793,-12.067,28.013
V,1265,37.960,-28.379,-57.668,-26.009,-86.579,24.535
W,1235,16.715,-36.120,-60.735,-52.309,-53.233,4.925
Y,1246,41.000,-9.901,-28.512,-8.710,-17.566,21.549
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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons