Fig. 4
From: Tpgen: a language model for stable protein design with a specific topology structure
Evaluation of the results for the stability of the sequences using molecular dynamics simulations. A Comparing the last frame of molecular dynamics simulation with the original structure, the generated results of TopoProGenerator showed a high degree of identity. B From Baker’s designed small proteins, our designed small proteins, RITA’s designed small proteins, and the RifDock HHH dataset, we selected 10 sequences with the lowest Rosetta energy scores. And we selected natural HHH protein 2kzi as the natural baseline. Subsequently, we performed molecular dynamics simulations to compare the selected sequences based on the analysis of the RMSD curve and determined the most favourable sequence. The unit of time is nanoseconds(ns), and the graph is plotted by averaging the values of all data points within each nanosecond(ns)