(Sun, 01/19/2020 - 15:59 | 5 comments)
Which atoms does Wiggle Backbone move?
|Opened on:||Sunday, January 19, 2020 - 15:59|
|Last modified:||Sunday, February 9, 2020 - 19:44|
For all amino acids in Foldit, atoms 1-4 are backbone atoms. Are the H's hanging off the alpha-carbon and backbone nitrogen also considered backbone atoms? Are the extra H's and O's on the N- and C- terminal amino acids also considered backbone atoms? These H's and the extra O's won't have atom #'s from 1-4. Does Wiggle Backbone in Foldit only wiggle atoms 1-4 on each segment, or does it also wiggle the backbone and terminal H's and O's? Do the non-backbone (sidechain) atoms on each segment move together like a rigid body, rotating and translating as a unit, with the amount of rotation and translation set by the motions of the segment's backbone atoms? I ask because different amino acids will have different atom #'s for the backbone H's; for example, I think usually the H attached to cysteine's backbone N is atom 7 while the H attached to histidine's backbone N is atom 11. Does Wiggle Backbone keep all covalent bond lengths fixed? Does Wiggle Backbone just vary the phi,psi dihedral angles, since these angles (with fixed covalent bond lengths) are enough to determine the positions of all backbone atoms? Thanks!