Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity

Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020

(2021) Kathy Leung et al.   Eurosurveillance

Cold sensitivity of the SARS-CoV-2 spike ectodomain

(2021) Robert J. Edwards et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021

(2021) Summer E. Galloway et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines

(2021) Xiaoying Shen et al.   Cell Host & Microbe

Potent SARS-CoV-2 Neutralizing Antibodies Directed Against Spike N-Terminal Domain Target a Single Supersite

(2021) Gabriele Cerutti et al.   Cell Host & Microbe

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

(2021) Houriiyah Tegally et al.   NATURE

mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants

(2021) Zijun Wang et al.   NATURE

SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

(2021) Constantinos Kurt Wibmer et al.   NATURE MEDICINE

Neutralization of SARS-CoV-2 spike 69/70 deletion, E484K and N501Y variants by BNT162b2 vaccine-elicited sera

(2021) Xuping Xie et al.   NATURE MEDICINE

Detection of B.1.351 SARS-CoV-2 Variant Strain — Zambia, December 2020

(2021) Mulenga Mwenda et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

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

(2021) Matthew McCallum et al.   CELL

SARS-CoV-2 variants B.1.351 and P.1 escape from neutralizing antibodies

(2021) Markus Hoffmann et al.   CELL

Increased resistance of SARS-CoV-2 variant P.1 to antibody neutralization

(2021) Pengfei Wang et al.   Cell Host & Microbe

Novel SARS-CoV-2 variants: the pandemics within the pandemic

(2021) Erik Boehm et al.   CLINICAL MICROBIOLOGY AND INFECTION

Neutralizing antibody vaccine for pandemic and pre-emergent coronaviruses

(2021) Kevin O. Saunders et al.   NATURE

Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7

(2021) Nicholas G. Davies et al.   NATURE

Structural impact on SARS-CoV-2 spike protein by D614G substitution

(2021) Jun Zhang et al.   SCIENCE

Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2

(2020) Renhong Yan et al.   SCIENCE

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Pandemic Preparedness: Developing Vaccines and Therapeutic Antibodies For COVID-19

(2020) Gregory D. Sempowski et al.   CELL

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

(2020) Alexandra C. Walls et al.   CELL

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

(2020) Markus Hoffmann et al.   CELL

A Multibasic Cleavage Site in the Spike Protein of SARS-CoV-2 Is Essential for Infection of Human Lung Cells

(2020) Markus Hoffmann et al.   MOLECULAR CELL

Cell entry mechanisms of SARS-CoV-2

(2020) Jian Shang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells

(2020) Shutoku Matsuyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Tyler N. Starr et al.   CELL

Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies

(2020) Christopher O. Barnes et al.   CELL

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

(2020) Bette Korber et al.   CELL

Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

(2020) Hyeonuk Woo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness

(2020) Kizzmekia S. Corbett et al.   NATURE

Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike

(2020) Lihong Liu et al.   NATURE

Controlling the SARS-CoV-2 spike glycoprotein conformation

(2020) Rory Henderson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Bio3D Packages for Structural Bioinformatics

(2020) Barry J. Grant et al.   PROTEIN SCIENCE

Structural basis of a shared antibody response to SARS-CoV-2

(2020) Meng Yuan et al.   SCIENCE

TMPRSS2 and furin are both essential for proteolytic activation of SARS-CoV-2 in human airway cells

(2020) Dorothea Bestle et al.   Life Science Alliance

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

(2020) Leonid Yurkovetskiy et al.   CELL

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

(2020) Christopher O. Barnes et al.   NATURE

Structures and distributions of SARS-CoV-2 spike proteins on intact virions

(2020) Zunlong Ke et al.   NATURE

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

(2020) Beata Turoňová et al.   SCIENCE

Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains

(2020) Tongqing Zhou et al.   Cell Host & Microbe

SARS-CoV-2 and the human-animal interface: outbreaks on mink farms

(2020) Marion Koopmans   LANCET INFECTIOUS DISEASES

Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil

(2020) Marcelo Henrique Santos Paiva et al.   Viruses-Basel

D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction

(2020) Sophie M.-C. Gobeil et al.   Cell Reports

A New Crystal Form of the SARS-CoV-2 Receptor Binding Domain: CR3022 Complex—An Ideal Target for In-Crystal Fragment Screening of the ACE2 Binding Site Surface

(2020) Charlie Nichols et al.   Frontiers in Pharmacology

Variational Approach for Learning Markov Processes from Time Series Data

(2019) Hao Wu et al.   JOURNAL OF NONLINEAR SCIENCE

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

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

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

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

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

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

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

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

Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains

(2017) Yuan Yuan et al.   Nature Communications

Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding

(2016) Miao Gui et al.   CELL RESEARCH

HTMD: High-Throughput Molecular Dynamics for Molecular Discovery

(2016) S. Doerr et al.   Journal of Chemical Theory and Computation

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

(2015) Chad W. Hopkins et al.   Journal of Chemical Theory and Computation

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

A highly stable prefusion RSV F vaccine derived from structural analysis of the fusion mechanism

(2015) Anders Krarup et al.   Nature Communications

Identification of slow molecular order parameters for Markov model construction

(2013) Guillermo Pérez-Hernández et al.   JOURNAL OF CHEMICAL PHYSICS

A Bayesian View on Cryo-EM Structure Determination

(2011) Sjors H.W. Scheres   JOURNAL OF MOLECULAR BIOLOGY

Features and development ofCoot

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

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY