Collective variable driven molecular dynamics to improve protein­ protein docking scoring.

DIEGO MASONE; SOLÈNE GROSDIDIER

COMPUTATIONAL BIOLOGY AND CHEMISTRY

ELSEVIER SCI LTD

Año: 2014 vol. 49 p. 1 - 6

1476-9271

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.