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Recipe: ST - glycine hinge
Created by Seagat2011 78 1584
3.9375
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Name: ST - glycine hinge
ID: 28374
Created on: Wed, 05/11/2011 - 08:46
Updated on: Mon, 05/16/2011 - 01:11
Description:

Because Glycine is the most flexible Amino acid, it will respond readily and rather predictably to manipulation. The "glycine hinge" is a tactic used to shape a section of a Loop containing at least one glycine. It is most useful when a player has some idea of where other secondary structures should go, and wants to bend the loop in a way that will put them in the appropriate places while not dragging down his local score too much.[1] Recipe attempts to freeze backbone, and necessary Secondary Structures (SS), ("The rods"), around the surrounding Glycine Amino Acid (AA), ("The hinge"), and proceeds to wiggle with bands.



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Joined: 08/24/2010
Hi

This recipe is also intended for Exploratory puzzles :)

Here are available recipe options

-------------- RECIPE OPTIONS --------------
wiggle_count = 1, -- #iters

allow_float_wiggle_count = false, -- allows "floating" via random number generation of wiggle_count

wiggle_count_upper = wiggle_count, -- max possible #iters. iff allow_float_wiggle_count, then this value must be defined. (disabled by default)

wiggle_count_lower = wiggle_count, -- min possible #iters. iff allow_float_wiggle_count, then this value must be defined. (disabled by default)

wiggle_count_bounds = wiggle_count, -- allowed variance for #iters. iff allow_float_wiggle_count, then this value must be defined. (disabled by default)

global_wiggle = true, -- perform wa. iff false, then perform lws (local_wiggle)

freeze_backbone = true, -- freeze bb

freeze_sidechains = false, -- freeze sc (disabled by default)

ci = 0.30, -- clashing importance

allow_ci_float = false, -- allows "floating" via random number generation of ci. Iff true, ci_upper and ci_lower must be defined. (disabled by default)

ci_upper = ci, -- U_ci_value. ff allow_ci_float == true, then this value must be defined. (disabled by default)

ci_lower = ci, -- L_ci_value. ff allow_ci_float == true, then this value must be defined. (disabled by default)

ci_bounds = ci, -- allowed variance for ci. ff allow_ci_float == true, then this value must be defined. (disabled by default)

exploratory = false, -- run on exploratory puzzles (disabled by default)

qs_recent_best = 3, -- iff exploratory == true, then recent best is saved into this saveslot

verbose = true, -- keep the user updated (enabled by default)

Cheers,
Seagate2011

Joined: 08/24/2010
*updated*

Updated - May 11, 2011

Fixed!

New features added:

range_enable = false, -- allows test-only in user-designated range

range_min = 0, -- idx = L_value. iff range_enable == true, then this value must be defined. (disabled by default)

range_max = 0, -- idx2 = R_value. iff range_enable == true, then this value must be defined. (disabled by default)

Joined: 08/24/2010
*updated*

updated - May 11, 2011 - version 1.1.2.1

New feature added:

freeze_hinge_instead = false, -- allows for the hinge to be frozen instead of the rods. (disabled by default)(pending evaluation)

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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, RosettaCommons