The blacksmith's profession is a worthy analogy for what Rice University scientists have wrought: A new method for making accurate structural models of proteins that takes far less computational power than existing brute-force approaches.
The goal of the structural models produced by computation, according to physicist Peter Wolynes of Rice's Center for Theoretical Biological Physics (CTBP), is to be as detailed and useful as those produced by laborious experimental means, particularly X-ray crystallography, that provide detailed locations for every atom within a protein.
The new method takes its inspiration from metallurgy.
Like the blacksmith who must not only heat and cool a metal but also strike the metal just right to move it closer to a useful product, the Rice project led by Wolynes and alumnus Xingcheng Lin applies force at strategic points during the simulation of protein models so as to speed up the computation.
"One big question is whether we could ever become more confident in the accuracy of the results of a simulation than the result of X-ray experiments," Wolynes said.
But crystal structures provide only a snapshot of a protein that in reality changes its global shape and detailed atomic positions as the protein carries out its work in the cell.