Browsing by Subject "Implicit solvent"

Now showing items 1-3 of 3

Article

Combination of theoretical and experimental approaches for the design and study of fibril-forming peptides

Tamamis, Phanourios; Kasotakis, E.; Archontis, Georgios Z.; Mitraki, A. (2014)

Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular interest to modern bionanotechnology and materials science. Their ability to form biocompatible ...
Article

Insights into the mechanism of C5aR inhibition by PMX53 via implicit solvent molecular dynamics simulations and docking

Tamamis, Phanourios; Kieslich, C. A.; Nikiforovich, G. V.; Woodruff, T. M.; Morikis, D.; Archontis, Georgios Z. (2014)

Background: The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. The cyclic hexapeptide PMX53 (sequence ...
Article

Proteus and the design of ligand binding sites

Polydorides, Savvas; Michael, E.; Mignon, D.; Druart, Karen; Archontis, Georgios Z.; Simonson, T. (2016)

This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding ...