Collective variable driven molecular dynamics to improve protein-protein docking scoring.
In biophysics, the structural prediction of protein-protein complexes starting from the unbound form of the two interacting monomers is a major difficulty. Although current computational docking protocols are able to generate near-native solutions in a reasonable time, the problem of identifying near-native conformations from a pool of solutions remains very challenging. In this study, we use molecular dynamics simulations driven by a collective reaction coordinate to optimize full hydrogen bond networks in a set of protein-protein docking solutions. The collective coordinate biases the system to maximize the formation of hydrogen bonds at the protein-protein interface as well as all over the structure. The reaction coordinate is therefore a measure for docking poses affinity and hence is used as scoring function to identify near-native conformations.
['Masone|Diego|D|', 'Grosdidier|Solène|S|']
D006860:Hydrogen Bonding D056004:Molecular Dynamics Simulation D011506:Proteins
Collective variable Molecular dynamics Docking Scoring Protein–protein