Paper Citing NAMD - Abstract
Bajaj, Chandrajit; Bauer, Benedikt; Bettadapura, Radhakrishna; Vollrath, Antje
NONUNIFORM FOURIER TRANSFORMS FOR RIGID-BODY AND MULTIDIMENSIONAL ROTATIONAL CORRELATIONS
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 35:B821-B845, 2013
The task of evaluating correlations is central to computational structural biology. The rigid-body correlation problem seeks the rigid-body transformation (R, t), R is an element of SO(3), t is an element of R-3, that maximizes the correlation between a pair of input scalar-valued functions representing molecular structures. Exhaustive solutions to the rigid-body correlation problem take advantage of the fast Fourier transform to achieve a speedup with respect to either the sought translation or rotation. We present PFcorr, a new exhaustive solution, based on the nonequispaced SO(3) Fourier transform, to the rigid-body correlation problem; unlike previous solutions, ours achieves a combination of translational and rotational speedups without requiring equispaced grids. PFcorr can be straightforwardly applied to a variety of problems in protein structure prediction and refinement that involve correlations under rigid-body motions of the protein. Additionally, we show how it applies, along with an appropriate flexibility model, to analogues of the above problems in which the flexibility of the protein is relevant.
