Limiting the EM steering potential to backbone atoms tends to moderate the contribution of the EM term in the simulated energy function, thus compensating for the limited number of experimental constraints available from our cryo-EM maps.
Table 3 Average percentage improvement in SD connections using the Morse potential for backbone-to-terminal links, with maximum transmitted power of 3 W, 5 W, and 7 W.
The success of such WMNs largely hinges on their potential for scaling backbone throughput with increasing client density while preserving network coverage.
This study demonstrates the potential of imposing backbone cyclization on bioactive peptomers as a promising approach in developing an orally available peptidomimetic drug leads.
All simulations were carried out using the NAMD program [61] with the CHARMM27 [58], [58] force field including the CMAP backbone potential.
We thus generated a reference ensemble of the GB1 domain using an MD simulation with the CHARMM22 topology format and force-field [42] with a modified backbone potential [43] and a generalized Born solvent model [44].
In this study, we used SMURF prediction to annotate potential gene cluster backbone enzymes in the B. papendorfii UM 226 genome.
Backbone potential describes the energy scores considering the interactions between atoms O3', C3', C4', C5', O5', P, OP1, OP2 and OP3 (36 atom types, 9 for each nucleotide).
The "refinement potentials" included the docking potentials, Xplor-NIH's RAMAchandran (backbone dihedral angle database) potential (23), and the HBDB (dynamic hydrogen bonding) potential (24).
