Fig. 1: Cartoon representation of the folding energy landscape comparing AlphaFold2’s smooth surface (left) with a rugged landscape typical of physics-based force fields (right).
From: Rapid estimation of protein folding pathways from sequence alone using AlphaFold2
In physics-based approaches, extensive sampling is required to identify the native basin, whereas in AF2, MSAs or protein templates quickly guide structure refinement to narrower regions of conformational space, effectively bypassing other regions. We employ an AF2-ab initio approach, iteratively generating structures with the help of last round prediction to navigate the smooth energy function learned by AF2 starting from single sequence alone. Source data are provided as a Source Data file.
