Optimal identification of semi-rigid domains in macromolecules from molecular dynamics simulation.

ABSTRACT: Biological function relies on the fact that biomolecules can switch between different conformations and aggregation states. Such transitions involve a rearrangement of parts of the biomolecules involved that act as dynamic domains. The reliable identification of such domains is thus a key problem in biophysics. In this work we present a method to identify semi-rigid domains based on dynamical data that can be obtained from molecular dynamics simulations or experiments. To this end the average inter-atomic distance-deviations are computed. The resulting matrix is then clustered by a constrained quadratic optimization problem. The reliability and performance of the method are demonstrated for two artificial peptides. Furthermore we correlate the mechanical properties with biological malfunct

SUBMITTER: Bernhard S 

PROVIDER: S-EPMC2869351 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature