RecCrysFormer: Refined Protein Structural Prediction from 3D Patterson Maps via Recycling Training Runs

Code

• github.com/sciadopitys/RecCrysFormer
  Officialpytorch★ 0

Abstract

Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce RecCrysFormer, a hybrid model that exploits the strengths of transformers with the aim of integrating experimental and ML approaches to protein structure determination from crystallographic data. RecCrysFormer leverages Patterson maps and incorporates known standardized partial structures of amino acid residues to directly predict electron density maps, which are essential for constructing detailed atomic models through crystallographic refinement processes. RecCrysFormer benefits from a ``recycling'' training regimen that iteratively incorporates results from crystallographic refinements and previous training runs as additional inputs in the form of template maps. Using a preliminary dataset of synthetic peptide fragments based on Protein Data Bank, RecCrysFormer achieves good accuracy in structural predictions and shows robustness against variations in crystal parameters, such as unit cell dimensions and angles.

Reproductions