Alexandre Urzhumtsev

Variable Resolution Maps (VRM) in CCTBX and Phenix: Accounting For Local Resolution In cryoEM

The paper implements a method in CCTBX and Phenix to calculate variable-resolution maps from atomic models, improving accuracy by incorporating local resolution and atomic parameters.

EXPLICIT CORRECTION OF SEVERELY NON-UNIFORM DISTRIBUTIONS OF CRYO-EM VIEWS

This paper improves 3D cryo-EM reconstructions by explicitly correcting non-uniform distributions of 2D projections using the VUE program.

QUANTIFYING DISTRIBUTIONS OF CRYO-EM PROJECTIONS

The paper introduces a numerical measure to quantify the deviation of cryo-EM 2D view distributions from uniformity, replacing traditional 2D diagrams with 1D curves for standardized analysis.

DIRECT CALCULATION OF VARIABLE-RESOLUTION MAPS BY FULLY ANALYTIC APPROXIMATIONS TO ATOMIC IMAGES

The paper introduces a method to calculate variable-resolution maps using analytic shell-function approximations to atomic images, enabling comparison with experimental cryo-EM maps.

Straightening FSC curves

The paper introduces a new scale for plotting FSC curves that ensures consistent statistics and improves reliability of high-resolution values.

Analytic representation of inhomogeneous-resolution maps of three-dimensional scalar fields

The paper develops an analytic method to generate inhomogeneous-resolution maps for refining atomic models in structural biology and other fields.

A mosaic bulk-solvent model improves density maps and the fit between model and data

The paper introduces a mosaic bulk-solvent model that improves the fit between crystallographic models and data, enhancing density map quality and solving previously inaccessible problems.

Including Crystallographic Symmetry in Quantum-based Refinement: Q|R#2

The paper refines a protein structure using quantum chemistry restraints, incorporating crystallographic symmetry effects through a fragmentation approach.

New tools for the analysis and validation of Cryo-EM maps and atomic models

The paper introduces new computational tools for validating cryo-EM maps and atomic models, including methods for resolution estimation, map sharpening, and map analysis.

Real-space refinement in Phenix for cryo-EM and crystallography

The paper describes real-space refinement in Phenix for improving cryo-EM models using additional restraints and shows significant model improvement.