Learn More
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)
Electron microscopy is used to reveal the structure of brain tissue at the micron and submicron scale. However, structural analysis of the spatial relationships between various cellular structures as well as the arrangement of organelles within cells is limited in two-dimensional electron microscopy images. Reconstruction from serial section transmission(More)
Envelope glycoprotein gp120 of HIV-1 possesses several variable regions; their precise structure has been difficult to establish. We report a new model of gp120, in complex with antibodies CD4 and 17b, complete with its variable regions. The model was produced by a computational protocol that uses cryo-electron microscopy (EM) maps, atomic-resolution(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)
  • 1