Abstract
Molecular docking outshines other approaches at creating a surfeit of
potential models of protein-protein complexes. It is highly challenging
to distinguish the favourable, native-like models from the newly
discovered ones. We propose here a protocol based on molecular dynamics
(MD) simulations that would allow distinguishing native from non-native
models to complement scoring functions used in docking. The initial part
of the study concentrated on modelling the protein-protein complex of a
cyclic peptide (cter M) from Clitoria ternatea with Daboia
ruselli snake venom PLA 2 receptor using docking in
Discovery Studio, which was complemented with molecular dynamic
simulations to discriminate between native protein and the investigated
complex to report its stability. The peptide complex showed almost
similar stability in nearly all measured properties, such as Root Mean
Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius
of Gyration (Rg) of native contacts from the initial docked model. A
reasonably short simulation of 100 ns is sufficient to achieve this
accuracy, making this approach practical.