SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape

Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody

(2021) C. Garrett Rappazzo et al.   SCIENCE

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

(2021) Tyler N. Starr et al.   SCIENCE

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E

(2021) Kathryn E Kistler et al.   eLife

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

(2021) Emma C. Thomson et al.   CELL

Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions for optimal therapeutic protection

(2021) Emma S. Winkler et al.   CELL

Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization

(2021) Zhuoming Liu et al.   Cell Host & Microbe

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

(2021) Allison J. Greaney et al.   Cell Host & Microbe

Emergence of a Novel SARS-CoV-2 Variant in Southern California

(2021) Wenjuan Zhang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

(2021) Dami A. Collier et al.   NATURE

Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein

(2021) Houriiyah Tegally et al.   NATURE

Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7

(2021) Pengfei Wang et al.   NATURE

Resistance of SARS-CoV-2 variants to neutralization by monoclonal and serum-derived polyclonal antibodies

(2021) Rita E. Chen et al.   NATURE MEDICINE

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

(2021) Matthew McCallum et al.   CELL

Neutralizing antibody vaccine for pandemic and pre-emergent coronaviruses

(2021) Kevin O. Saunders et al.   NATURE

Structural basis for broad coronavirus neutralization

(2021) Maximilian M. Sauer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

(2021) Nuno R. Faria et al.   SCIENCE

A human coronavirus evolves antigenically to escape antibody immunity

(2021) Rachel T. Eguia et al.   PLoS Pathogens

Tackling COVID-19 with neutralizing monoclonal antibodies

(2021) Davide Corti et al.   CELL

Broad sarbecovirus neutralization by a human monoclonal antibody

(2021) M. Alejandra Tortorici et al.   NATURE

SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

(2021) Maxwell I. Zimmerman et al.   Nature Chemistry

SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern

(2021) Matthew McCallum et al.   SCIENCE

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses

(2020) Michael Letko et al.   Nature Microbiology

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

(2020) Alexandra C. Walls et al.   CELL

A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein

(2020) Hong Zhou et al.   CURRENT BIOLOGY

A human neutralizing antibody targets the receptor binding site of SARS-CoV-2

(2020) Rui Shi et al.   NATURE

Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody

(2020) Dora Pinto et al.   NATURE

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor

(2020) Jun Lan et al.   NATURE

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins

(2020) Tommy Tsan-Yuk Lam et al.   NATURE

Site-specific glycan analysis of the SARS-CoV-2 spike

(2020) Yasunori Watanabe et al.   SCIENCE

A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV

(2020) Meng Yuan et al.   SCIENCE

Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays

(2020) Katharine H. D. Crawford et al.   Viruses-Basel

Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

(2020) Tyler N. Starr et al.   CELL

A SARS-CoV-2 Infection Model in Mice Demonstrates Protection by Neutralizing Antibodies

(2020) Ahmed O. Hassan et al.   CELL

Neutralizing Antibody and Soluble ACE2 Inhibition of a Replication-Competent VSV-SARS-CoV-2 and a Clinical Isolate of SARS-CoV-2

(2020) James Brett Case et al.   Cell Host & Microbe

Mitigating local over-fitting during single particle reconstruction with SIDESPLITTER

(2020) Kailash Ramlaul et al.   JOURNAL OF STRUCTURAL BIOLOGY

Potently neutralizing and protective human antibodies against SARS-CoV-2

(2020) Seth J. Zost et al.   NATURE

Structure-based design of prefusion-stabilized SARS-CoV-2 spikes

(2020) Ching-Lin Hsieh et al.   SCIENCE

Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail

(2020) Johanna Hansen et al.   SCIENCE

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology

(2020) Luca Piccoli et al.   CELL

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

(2020) Christopher O. Barnes et al.   NATURE

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

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

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms

(2020) M. Alejandra Tortorici et al.   SCIENCE

A nanoluciferase SARS-CoV-2 for rapid neutralization testing and screening of anti-infective drugs for COVID-19

(2020) Xuping Xie et al.   Nature Communications

Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

(2020) Allison J. Greaney et al.   Cell Host & Microbe

Antibody potency, effector function, and combinations in protection and therapy for SARS-CoV-2 infection in vivo

(2020) Alexandra Schäfer et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A single-dose live-attenuated YF17D-vectored SARS-CoV-2 vaccine candidate

(2020) Lorena Sanchez-Felipe et al.   NATURE

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

(2020) Ali Punjani et al.   NATURE METHODS

STAT2 signaling restricts viral dissemination but drives severe pneumonia in SARS-CoV-2 infected hamsters

(2020) Robbert Boudewijns et al.   Nature Communications

An Antigenic Atlas of HIV-1 Escape from Broadly Neutralizing Antibodies Distinguishes Functional and Structural Epitopes

(2019) Adam S. Dingens et al.   IMMUNITY

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

(2019) Alexandra C. Walls et al.   CELL

Real-time cryo-electron microscopy data preprocessing with Warp

(2019) Dimitry Tegunov et al.   NATURE METHODS

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

(2019) Ana Casañal et al.   PROTEIN SCIENCE

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

Inferring the shape of global epistasis

(2018) Jakub Otwinowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Jasenko Zivanov et al.   eLife

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

(2018) Jasenko Zivanov et al.   IUCrJ

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

(2016) Ray Yu-Ruei Wang et al.   eLife

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

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

(2015) James A. Maier et al.   Journal of Chemical Theory and Computation

A Haploid Genetic Screen Identifies Heparan Sulfate Proteoglycans Supporting Rift Valley Fever Virus Infection

(2015) Amber M. Riblett et al.   JOURNAL OF VIROLOGY

A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence

(2015) Vineet D Menachery et al.   NATURE MEDICINE

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Robust and efficient configurational molecular sampling via Langevin dynamics

(2013) Benedict Leimkuhler et al.   JOURNAL OF CHEMICAL PHYSICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

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