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We review tools for structure identification and model-based refinement from three-dimensional electron microscopy implemented in our in-house software package, VOLROVER 2.0. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric, and monomeric subunits using techniques based on automatic symmetry detection and multidomain fast… (More)

The task of evaluating correlations is central to computational structural biology. The rigid-body correlation problem seeks the rigid-body transformation (R, t), R ∈ SO(3), t ∈ 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… (More)

Whereas traditional finite element methods use meshes to define domain geometry, weighted extended B-spline finite element methods rely on a weight function. A weight function is a smooth, strictly positive function which vanishes at the domain boundary at an appropriate rate. We describe a method for generating weight functions for a general class of… (More)

We present the data used for an integrative approach to computational modeling of proteins with large variable domains, specifically applied in this context to model HIV Env glycoprotein gp120 in its CD4 and 17b bound state. The initial data involved X-ray structure PDBID:1GC1 and electron microscopy image EMD:5020. Other existing X-ray structures were used… (More)

There continue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstructed from X-ray diffraction or NMR data), and 3D reconstructed cryo-electron microscopy (3D EM) maps (albeit at coarser resolution) of the same or homologous molecule or molecular assembly, deposited in the EMDB. To obtain the best possible… (More)

- Radhakrishna Bettadapura, Tim Mashburn, Richard Crawford
- 2013

We study the curve smoothing problem in the context of Bézier curves of constant length. Specifically , we present a degree-independent simulated annealing based technique to smooth a length-constrained Bézier curve with arbitrary, user-specified geometric constraints. Smoothing is accomplished in two stages. First, a generalized degree-independent… (More)

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