Architecture and self-assembly of the jumbo bacteriophage nuclear shell

Anti-CRISPRs go viral: the infection biology of CRISPR-Cas inhibitors

(2021) Yuping Li et al.   Cell Host & Microbe

Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts

(2021) Lakshminarayan M. Iyer et al.   Viruses-Basel

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells

(2021) Dimitry Tegunov et al.   NATURE METHODS

Selective transport of fluorescent proteins into the phage nucleus

(2021) Katrina T. Nguyen et al.   PLoS One

Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo

(2021) Stefano Scaramuzza et al.   PLOS BIOLOGY

A flexible framework for multi-particle refinement in cryo-electron tomography

(2021) Alister Burt et al.   PLOS BIOLOGY

The arms race between bacteria and their phage foes

(2020) Hannah G. Hampton et al.   NATURE

Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1

(2020) Jasenko Zivanov et al.   IUCrJ

A Cut above the Rest: Characterization of the Assembly of a Large Viral Icosahedral Capsid

(2020) Erin R. Reilly et al.   Viruses-Basel

Reliable estimation of membrane curvature for cryo-electron tomography

(2020) Maria Salfer et al.   PLoS Computational Biology

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

The Mottled Capsid of the Salmonella Giant Phage SPN3US, a Likely Maturation Intermediate with a Novel Internal Shell

(2020) J. Bernard Heymann et al.   Viruses-Basel

Maturation of Pseudo-Nucleus Compartment in P. aeruginosa, Infected with Giant phiKZ Phage

(2020) Yana A. Danilova et al.   Viruses-Basel

Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction

(2020) Ali Punjani et al.   NATURE METHODS

DeepTracer for fast de novo cryo-EM protein structure modeling and special studies on CoV-related complexes

(2020) Jonas Pfab et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal Structure of the Enterohemorrhagic Escherichia coli AtaT-AtaR Toxin-Antitoxin Complex

(2019) Yuka Yashiro et al.   STRUCTURE

(Ph)ighting Phages: How Bacteria Resist Their Parasites

(2019) Jakob T. Rostøl et al.   Cell Host & Microbe

DaReUS-Loop: a web server to model multiple loops in homology models

(2019) Yasaman Karami et al.   NUCLEIC ACIDS RESEARCH

Viral Capsid Trafficking along Treadmilling Tubulin Filaments in Bacteria

(2019) Vorrapon Chaikeeratisak et al.   CELL

CHAP: A Versatile Tool for the Structural and Functional Annotation of Ion Channel Pores

(2019) Gianni Klesse et al.   JOURNAL OF MOLECULAR BIOLOGY

In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release

(2019) Ke Ding et al.   Nature Communications

Normal Mode Analysis as a Routine Part of a Structural Investigation

(2019) Jacob A. Bauer et al.   MOLECULES

Real-time cryo-electron microscopy data preprocessing with Warp

(2019) Dimitry Tegunov et al.   NATURE METHODS

ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution

(2019) Chuan Tian et al.   Journal of Chemical Theory and Computation

A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases

(2019) Senén D. Mendoza et al.   NATURE

A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity

(2019) Lucia M. Malone et al.   Nature Microbiology

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

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

Only a Subset of Normal Modes is Sufficient to Identify Linear Correlations in Proteins

(2018) Mustafa Tekpinar et al.   Journal of Chemical Information and Modeling

Structure of the membrane-assembled retromer coat determined by cryo-electron tomography

(2018) Oleksiy Kovtun et al.   NATURE

Global proteomic profiling of Salmonella infection by a giant phage

(2018) Susan T. Weintraub et al.   JOURNAL OF VIROLOGY

A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis

(2018) Jasenko Zivanov et al.   IUCrJ

Dynamo Catalogue : Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms

(2017) Daniel Castaño-Díez et al.   JOURNAL OF STRUCTURAL BIOLOGY

Automated tilt series alignment and tomographic reconstruction in IMOD

(2017) David N. Mastronarde et al.   JOURNAL OF STRUCTURAL BIOLOGY

Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging

(2017) Wim J.H. Hagen et al.   JOURNAL OF STRUCTURAL BIOLOGY

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

(2017) Yong Zi Tan et al.   NATURE METHODS

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams et al.   PROTEIN SCIENCE

Improvements to the APBS biomolecular solvation software suite

(2017) Elizabeth Jurrus et al.   PROTEIN SCIENCE

Assembly of a nucleus-like structure during viral replication in bacteria

(2017) Vorrapon Chaikeeratisak et al.   SCIENCE

The Phage Nucleus and Tubulin Spindle Are Conserved among Large Pseudomonas Phages

(2017) Vorrapon Chaikeeratisak et al.   Cell Reports

Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions

(2015) Ivet Bahar et al.   BIOPHYSICAL JOURNAL

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model

(2015) Pengfei Li et al.   Journal of Chemical Theory and Computation

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

(2015) Benjamin A Barad et al.   NATURE METHODS

Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging

(2015) Tanmay A.M. Bharat et al.   STRUCTURE

Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes

(2015) Serban L. Ilca et al.   Nature Communications

Evol and ProDy for bridging protein sequence evolution and structural dynamics

(2014) A. Bakan et al.   BIOINFORMATICS

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Robust membrane detection based on tensor voting for electron tomography

(2014) Antonio Martinez-Sanchez et al.   JOURNAL OF STRUCTURAL BIOLOGY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy

(2013) Shaoxia Chen et al.   ULTRAMICROSCOPY

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Elastic Network Models Are Robust to Variations in Formalism

(2012) Nicholas Leioatts et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments

(2012) Daniel Castaño-Díez et al.   JOURNAL OF STRUCTURAL BIOLOGY

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

PBAD-Based Shuttle Vectors for Functional Analysis of Toxic and Highly Regulated Genes in Pseudomonas and Burkholderia spp. and Other Bacteria

(2008) D. Qiu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY