ColabFold

Question

[Preeti]

What does use_amber affect in ColabFold and what are relaxed and unrelaxed (structures?) mean?

Answer 1

[dthorbur]

AMBER force-field is a simulation of the atoms based on chemical principles used to "relax" the protein sequence. This process removes physically impossible occlusions of atoms, but does not improve the accuracy of the atom-to-atom distance measures. Here is an important paper describing the process.

Essentially, the use_amber flag is an optional post-processing step to slightly refine models. Ultimately, this process is not that important in most use cases but doesn't hurt to include if you have the capacity and aren't in a rush.