Structure of the bacterial ribosome at 2 Å resolution

Molecular analysis of the ribosome recycling factor ABCE 1 bound to the 30S post‐splitting complex

(2020) Elina Nürenberg‐Goloub et al.   EMBO JOURNAL

Clades of huge phages from across Earth’s ecosystems

(2020) Basem Al-Shayeb et al.   NATURE

Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit

(2020) Vanja Stojković et al.   NUCLEIC ACIDS RESEARCH

Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection

(2020) Justin C. Morse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome.

(2020) Evgeny B Pichkur et al.   RNA

Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading

(2020) Anna B. Loveland et al.   NATURE

Biosynthesis and Chemical Applications of Thioamides

(2019) Nilkamal Mahanta et al.   ACS Chemical Biology

Software tools for automated transmission electron microscopy

(2019) Martin Schorb et al.   NATURE METHODS

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Translation of Diverse Aramid- and 1,3-Dicarbonyl-peptides by Wild Type Ribosomes in Vitro

(2019) Omer Ad et al.   ACS Central Science

O-Methyltransferase-mediated Incorporation of a β-Amino Acid in Lanthipeptides

(2019) Jeella Z. Acedo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Modification at the 2′-Position of the 4,5-Series of 2-Deoxystreptamine Aminoglycoside Antibiotics To Resist Aminoglycoside Modifying Enzymes and Increase Ribosomal Target Selectivity

(2019) Girish C. Sati et al.   ACS Infectious Diseases

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

(2019) Dorothee Liebschner et al.   Acta Crystallographica Section D-Structural Biology

CryoEM maps are full of potential

(2019) Mayra A Marques et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Ribosome assembly defects subvert initiation Factor3 mediated scrutiny of bona fide start signal

(2019) Himanshu Sharma et al.   NUCLEIC ACIDS RESEARCH

Current Developments in Coot for Macromolecular Model Building of Electron Cryo‐microscopy and Crystallographic Data

(2019) Ana Casañal et al.   PROTEIN SCIENCE

Structure of ribosome-bound azole-modified peptide phazolicin rationalizes its species-specific mode of bacterial translation inhibition

(2019) Dmitrii Y. Travin et al.   Nature Communications

Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant

(2019) Yehuda Halfon et al.   Scientific Reports

Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts

(2019) Petr Tesina et al.   EMBO JOURNAL

Analysis of Global and Site-Specific Radiation Damage in Cryo-EM

(2018) Johan Hattne et al.   STRUCTURE

Ewald sphere correction using a single side-band image processing algorithm

(2018) Christopher J. Russo et al.   ULTRAMICROSCOPY

The Essential Genome of Escherichia coli K-12

(2018) Emily C. A. Goodall et al.   mBio

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

(2018) Takanori Nakane et al.   eLife

Studies on Aminoglycoside Susceptibility Identify a Novel Function of KsgA To Secure Translational Fidelity during Antibiotic Stress

(2018) Jin Zou et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

High resolution single particle cryo-electron microscopy using beam-image shift

(2018) Anchi Cheng et al.   JOURNAL OF STRUCTURAL BIOLOGY

Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale

(2018) Jane S. Richardson et al.   JOURNAL OF STRUCTURAL BIOLOGY

New tools for automated high-resolution cryo-EM structure determination in RELION-3

(2018) Jasenko Zivanov et al.   eLife

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database

(2017) Yunxiang Dai et al.   JOURNAL OF PROTEOME RESEARCH

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

(2017) Lindsay K. Pino et al.   MASS SPECTROMETRY REVIEWS

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

(2017) Shawn Q Zheng et al.   NATURE METHODS

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

(2017) Andy T Kong et al.   NATURE METHODS

Advances in the field of single-particle cryo-electron microscopy over the last decade

(2017) Joachim Frank   Nature Protocols

Crystal structure of eukaryotic ribosome and its complexes with inhibitors

(2017) Gulnara Yusupova et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ribosome dynamics during decoding

(2017) Marina V. Rodnina et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

N6′, N6′′′, and O4′ Modifications to Neomycin Affect Ribosomal Selectivity without Compromising Antibacterial Activity

(2017) Girish C. Sati et al.   ACS Infectious Diseases

A simple method to control over-alignment in the MAFFT multiple sequence alignment program

(2016) Kazutaka Katoh et al.   BIOINFORMATICS

Resolution advances in cryo-EM enable application to drug discovery

(2016) Sriram Subramaniam et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Emerging Roles of Protein Deamidation in Innate Immune Signaling

(2016) Jun Zhao et al.   JOURNAL OF VIROLOGY

EMPIAR: a public archive for raw electron microscopy image data

(2016) Andrii Iudin et al.   NATURE METHODS

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

(2016) Karthik Anantharaman et al.   Nature Communications

Bacterial Protein Synthesis as a Target for Antibiotic Inhibition

(2016) Stefan Arenz et al.   Cold Spring Harbor Perspectives in Medicine

RNA protects a nucleoprotein complex against radiation damage

(2016) Charles S. Bury et al.   Acta Crystallographica Section D-Structural Biology

Assessing and maximizing data quality in macromolecular crystallography

(2015) P Andrew Karplus et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

Structure of the E. coli ribosome–EF-Tu complex at

(2015) Niels Fischer et al.   NATURE

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-resolution structure of the Escherichia coli ribosome

(2015) Jonas Noeske et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

(2015) Eric W. Deutsch et al.   Proteomics Clinical Applications

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions

(2015) Michael R. Wasserman et al.   Nature Communications

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-resolution structure of the Escherichia coli ribosome

(2015) Jonas Noeske et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome

(2014) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli

(2014) Dipali G Sashital et al.   eLife

The ribosome as a versatile catalyst: reactions at the peptidyl transferase center

(2013) Marina V Rodnina   CURRENT OPINION IN STRUCTURAL BIOLOGY

A role for 16S rRNA dimethyltransferase (ksgA) in intrinsic clarithromycin resistance in Mycobacterium tuberculosis

(2013) Saranya Phunpruch et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Role of the Ribosomal P-Site Elements of m2G966, m5C967, and the S9 C-Terminal Tail in Maintenance of the Reading Frame during Translational Elongation in Escherichia coli

(2013) S. Arora et al.   JOURNAL OF BACTERIOLOGY

Cryo-EM model validation using independent map reconstructions

(2013) Frank DiMaio et al.   PROTEIN SCIENCE

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Staphylococcus aureus and Escherichia coli have disparate dependences on KsgA for growth and ribosome biogenesis

(2012) Heather C O’Farrell et al.   BMC MICROBIOLOGY

Deletion of gene encoding methyltransferase (gidB) confers high-level antimicrobial resistance in Salmonella

(2012) Dareen M Mikheil et al.   JOURNAL OF ANTIBIOTICS

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

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

Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans

(2012) Wei Ge et al.   Nature Chemical Biology

One core, two shells: bacterial and eukaryotic ribosomes

(2012) Sergey Melnikov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Allosteric control of the ribosome by small-molecule antibiotics

(2012) Leyi Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Outcome of the First Electron Microscopy Validation Task Force Meeting

(2012) Richard Henderson et al.   STRUCTURE

Control of Substrate Specificity by a Single Active Site Residue of the KsgA Methyltransferase

(2011) Heather C. O’Farrell et al.   BIOCHEMISTRY

Flexizymes for genetic code reprogramming

(2011) Yuki Goto et al.   Nature Protocols

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding

(2011) J. A. Dunkle et al.   SCIENCE

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

A Proteomic and Transcriptomic Approach Reveals New Insight into β-methylthiolation ofEscherichia coliRibosomal Protein S12

(2010) Michael Brad Strader et al.   MOLECULAR & CELLULAR PROTEOMICS

Hyperaccurate and Error-Prone Ribosomes Exploit Distinct Mechanisms during tRNA Selection

(2010) Hani S. Zaher et al.   MOLECULAR CELL

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Navigating the ribosome's metastable energy landscape

(2009) James B. Munro et al.   TRENDS IN BIOCHEMICAL SCIENCES

Inactivation of KsgA, a 16S rRNA Methyltransferase, Causes Vigorous Emergence of Mutants with High-Level Kasugamycin Resistance

(2008) K. Ochi et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Modified Uridines with C5-methylene Substituents at the First Position of the tRNA Anticodon Stabilize U·G Wobble Pairing during Decoding

(2008) Shinya Kurata et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanistic insight into the ribosome biogenesis functions of the ancient protein KsgA

(2008) Keith Connolly et al.   MOLECULAR MICROBIOLOGY

RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli

(2008) B. P. Anton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA backbone: Consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)

(2008) J. S. Richardson et al.   RNA