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primaryodors / primarydock

PrimaryOdors.org molecular docker.
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Pepteditor: Update CTNRG to allow omnidirectional optimization. #315

Open primaryodors opened 12 months ago

primaryodors commented 12 months ago

When two protein strands are placed in proximity to each other in 3D space, the CTNRG command measures their inter-strand binding energy with an option to move the second strand along an axis of motion to optimize that energy level.

A new option will be created that replaces the @direction parameter with a keyword such as FREE meaning the optimization motions are not constrained to any axis, but that the second protein may be freely nudged in any direction to achieve the most favorable binding energy.

An additional keyword may be implemented that denotes not only the possibility of free translation in all directions, but also slight rotations about the axis between the two residues at any given time with the strongest inter-strand binding energy.

primaryodors commented 12 months ago

Keyword FIND means change the direction of motion every iteration to look for the best fit.

Keyword FREE means do the same as FIND plus also attempt small rotations around the best contact pair.