Pipeline for the refinement of predicted protein structures and evaluation of their accuracy

Most 3D crystal structures for proteins of eukaryotes come from human and model organisms such as mouse, fruit fly and yeast. Until recently, there has been no method to acquire 3D protein structure for other organism such as parasitic worms and other pathogens.

The program AlphaFold, developed by DeepMind and published in July 2021, is about to "close the gap" between the quality of predicted proteins structure to those acquired from crystal structures. However, despite the progress, many predicted protein structures do not exhibit sufficient accuracy for applications such as drug design. To address this we need to refine structures using molecular dynamics (MD) simulations.

This project will develop a software pipeline for the refinement of predicted protein structures and the evaluation of their accuracy.