Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples

Could Egg White Lysozyme be Solved by Single Particle Cryo-EM?

(2020) Y. Zhang et al.   Journal of Chemical Information and Modeling

grand: A Python Module for Grand Canonical Water Sampling in OpenMM

(2020) Marley L. Samways et al.   Journal of Chemical Information and Modeling

Atomic-resolution protein structure determination by cryo-EM

(2020) Ka Man Yip et al.   NATURE

Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials

(2018) Ming Du et al.   ULTRAMICROSCOPY

Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4 Å

(2017) Beata Turoňová et al.   JOURNAL OF STRUCTURAL BIOLOGY

Large-Scale Structure and Hyperuniformity of Amorphous Ices

(2017) Fausto Martelli et al.   PHYSICAL REVIEW LETTERS

An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology

(2016) Rebecca F. Thompson et al.   METHODS

A precision cryostat design for manual and semi-automated cryo-plunge instruments

(2016) Christopher J. Russo et al.   REVIEW OF SCIENTIFIC INSTRUMENTS

Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data

(2016) Daniël M. Pelt et al.   JOURNAL OF SYNCHROTRON RADIATION

MULTEM: A new multislice program to perform accurate and fast electron diffraction and imaging simulations using Graphics Processing Units with CUDA

(2015) I. Lobato et al.   ULTRAMICROSCOPY

Thon rings from amorphous ice and implications of beam-induced Brownian motion in single particle electron cryo-microscopy

(2015) G. McMullan et al.   ULTRAMICROSCOPY

The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

(2015) Wim van Aarle et al.   ULTRAMICROSCOPY

Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions

(2015) Alan Brown et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

TomoPy: a framework for the analysis of synchrotron tomographic data

(2014) Dogˇa Gürsoy et al.   JOURNAL OF SYNCHROTRON RADIATION

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Image formation modeling in cryo-electron microscopy

(2013) Miloš Vulović et al.   JOURNAL OF STRUCTURAL BIOLOGY

REFMAC5 for the refinement of macromolecular crystal structures

(2011) Garib N. Murshudov et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?

(2009) Han Wang et al.   EUROPEAN PHYSICAL JOURNAL E

Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging

(2009) Giulia Zanetti et al.   JOURNAL OF STRUCTURAL BIOLOGY

Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution

(2008) Daniel Studer et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Restoration of weak phase-contrast images recorded with a high degree of defocus: The “twin image” problem associated with CTF correction

(2008) Kenneth H. Downing et al.   ULTRAMICROSCOPY