Alphafold-driven coarse grained dynamics

J. Beránek, V. Spiwok

University of Chemistry and Technology, Prague, Czech Republic

Jan1.Beranek@vscht.cz

AlphaFold 2.x is a useful tool for anyone working in structural biology or related fields. AlphaFold is great at predicting structures of proteins together with confidence scores. Maybe less well-known feature is that AlphaFold can be used also to predict probability distributions of distances of all pairs of amino acid residues in the predicted structure. We use this Alpha Fold output to infer the intramolecular potentials acting on the protein of interest. Suchinformation combined with coarse-graining of the molecule can be used to generate pseudo-trajectories of the protein, predicting the dynamics, of the secondary structures, multi-domain interaction or evaluating flexibility of intrinsically disordered parts of the structure. We show how this approach works on several systems.

This work was supported by Czech Science Foundation (22-29667S) and by COST Action ML4NGP, CA21160, . Computational resources were provided by the e-INFRA CZ project (ID:90254), supported by the Ministry of Education, Youth and Sports of the Czech Republic.