Optimal superpositioning of flexible molecule ensembles.

ABSTRACT: Analysis of the internal dynamics of a biological molecule requires the successful removal of overall translation and rotation. Particularly for flexible or intrinsically disordered peptides, this is a challenging task due to the absence of a well-defined reference structure that could be used for superpositioning. In this work, we started the analysis with a widely known formulation of an objective for the problem of superimposing a set of multiple molecules as variance minimization over an ensemble. A negative effect of this superpositioning method is the introduction of ambiguous rotations, where different rotation matrices may be applied to structurally similar molecules. We developed two algorithms to resolve the suboptimal rotations. The first approach minimizes the variance together

SUBMITTER: Gapsys V 

PROVIDER: S-EPMC3540257 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature