title: Collective variable driven molecular dynamics to improve protein-protein docking scoring.
abstract: 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.
authors: Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Ciencias Básicas (ICB), Universidad Nacional de Cuyo (UNCUYO), Mendoza, Argentina. Electronic address: dmasone@fing.uncu.edu.ar.
authors: Diego
authors: D
authors: Masone
authors: Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), DCEXS, Universitat Pompeu Fabra, Barcelona, Spain.
authors: Solène
authors: S
authors: Grosdidier
mesh_terms: D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D011506:Proteins
keywords: Collective variable; Docking; Molecular dynamics; Protein–protein; Scoring