Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge.

ABSTRACT: As the length of molecular dynamics (MD) trajectories grows with increasing computational power, so does the importance of clustering methods for partitioning trajectories into conformational bins. Of the methods available, the vast majority require users to either have some a priori knowledge about the system to be clustered or to tune clustering parameters through trial and error. Here we present non-parametric uses of two modern clustering techniques suitable for first-pass investigation of an MD trajectory. Being non-parametric, these methods require neither prior knowledge nor parameter tuning. The first method, HDBSCAN, is fast-relative to other popular clustering methods-and is able to group unstructured or intrinsically disordered systems (such as intrinsically disordered proteins,

SUBMITTER: Melvin RL 

PROVIDER: S-EPMC5719493 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature