t f is chosen when estimation quality, as measured by standard deviation, σ e 2, reaches a level considered sufficient/satisfying (Figure 8). Figure 8 Decreasing evolution of the standard deviation (blue line) calculated on windows of increasing dimension in the logarithmic time.
Fig. 2 Evolution of the standard deviation.
The evolution of the standard deviation parameter, with its narrowing followed by stabilizing, fits in with the idea that the rate coding may temporarily increase and consecutively adapt, resulting in a new balance.
Figure 4 shows the evolution of the estimated CFO standard deviation with the number of samples used in estimation algorithm (elements of ).
The time-dependent evolution of the root mean square deviations (RMSD) for the peptide C-α carbons, radius of gyration and secondary structure (i.e., analyzed using the DSSP criteria [75] for the peptide in the HFIP-water environment indicated when equilibrium was reached. Molecular model illustrations were rendered using PyMOL v0.99 (http://www.pymol.org).org
The time-dependent evolution of the root mean square deviations (RMSD) for the peptide α-Cs, radius of gyration and secondary structure (i.e., analyzed using the DSSP criteria [72] for the peptide in the HFIP-water environment indicated when equilibrium was reached. Molecular model structures were rendered using Rasmol version 2.7.4.2 (http://www.RasMol.org) and PyMOL v0.99 (http://www.pymol.org).org
The proteins have been analyzed in the last 10 ns of the trajectory (i.e. from 5 ns to 15 ns), where the three systems reach a conformational stability, as monitored by time evolution of the global Root Mean Square Deviation (RMSD), i.e. the displacement from the starting structure (see Figure S1 of Supplementary Data).
Unlike 3FTxs, where ASSET has played an important role in the evolution of new functions, deviation of some members of Kunitz-type serine protease inhibitors from protease inhibitory activity is mainly due to accelerated point mutations.
The time evolution of the enzyme backbone RMSD (root mean square deviation) in the product state compared to the lowest-energy conformation was calculated.
Figure S2 shows the evolution of the total energy and the root mean square deviation (RMSD) for both structures, during the last 10 ns of the equilibration period.
As well as the evolution of the mean telomere length, we consider the standard deviation and the shape of the distribution.
