The exclusion of the solvent exchange step yields soft mechanically fragile porous gels with structural limitations upon carbonization at high temperature in inert atmosphere, due to the surface tensions applied to the backbone during the evolution of volatiles.
Cooperative formation of α and β structures provided native-topology structures with the smallest backbone rmsd, 3.27 Å, to the NMR structure, although such structures were minority even when a knowledge-based force field was applied to the backbone dihedral potentials.
Our algorithm is applied to mesh backbone, and our target is optimizing links between mesh routers, i.e., relay links.
After this a further combination of 5000 steps of steepest descents and 5000 steps of conjugate gradients energy minimisation were carried out in which the same restraining force was applied to all backbone atoms only.
The side chains were then relaxed using several sequential minimizations with the force constants applied to the backbone atoms being decreased in each run.
To maintain the integrity of the secondary structure of the CG protomers, an internal elastic network was applied to the backbone beads of each residue, according to their secondary structure, as described in ref (17).
Secondly, the whole system was heated from 0 K to 300 K in water over 500 ps, with constraints applied to all backbone atoms, followed by 20 ns of simulation where the proteins were free to move.
In order to enhance sampling of internal and diffusive degrees of freedom, a dual boosting potential was applied to the backbone torsion angles and the overall boost potential as where Vt(r) is the total potential of the torsional terms, Vt(r) and Δ VT r) are the boost potentials applied to the torsional terms, and the total potential energy, respectively.
