Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes
Fig 9
Comparison of scores obtained by our interpenetration and scoring algorithm (ISA) and ROSETTA for a subset of structures.
We chose a random subset of structures from the expansion scheme simulations to score using ROSETTA and ISA. Rosetta scores range from −250 to ≈ 18 000 Rosetta Energy Units (REU). ROSETTA’s scoring functions with default weights support our claim that many structures exhibit lower scores, as the most structures can be found for lower scores where a high bin count can be observed (A). Our ISA algorithm correlates with the much more sophisticated ROSETTA algorithm with a Pearson correlation coefficient of 0.88 (B). However, our algorithm was 1000 times faster than pyROSETTA (both algorithms have been parallelized on a per-structure basis using the Python package joblib [69]).