Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining.

ABSTRACT: Coarse-graining is commonly used to decrease the computational cost of simulations. However, coarse-grained models are also considered to have lower transferability, with lower accuracy for systems outside the original scope of parametrization. Here, we benchmark a bead-necklace model and a modified Martini 2 model, both coarse-grained models, for a set of intrinsically disordered proteins, with the different models having different degrees of coarse-graining. The SOP-IDP model has earlier been used for this set of proteins; thus, those results are included in this study to compare how models with different levels of coarse-graining compare. The sometimes naive expectation of the least coarse-grained model performing best does not hold true for the experimental pool of proteins used here.

SUBMITTER: Fagerberg E 

PROVIDER: S-EPMC10336962 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature