Collective variable driven molecular dynamics to improve protein­ protein docking scoring

• Autores: Masone, Diego Fernando; Grosdidier, Solène
• Año de publicación: 2013
• Idioma: inglés
• Tipo de recurso: artículo
• Materia: Protein-Protein; Docking Scoring; Molecular Dynamics; Collective Variable; Scoring
• Institución: Consejo Nacional de Investigaciones Científicas y Técnicas

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.
Fil: Masone, Diego Fernando. Universidad Nacional de Cuyo. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentina
Fil: Grosdidier, Solène. Universitat Pompeu Fabra. Hospital del Mar Research Institute. Research Programme on Biomedical Informatics; España