Shifting mutational constraints in the SARS-CoV-2 receptor-binding domain during viral evolution

Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2

(2022) Pengcheng Han et al.   CELL

Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity

(2022) Bo Meng et al.   NATURE

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

(2022) Elisabetta Cameroni et al.   NATURE

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

(2022) Raquel Viana et al.   NATURE

ACE2 binding is an ancestral and evolvable trait of sarbecoviruses

(2022) Tyler N. Starr et al.   NATURE

A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy

(2022) Allison J. Greaney et al.   PLoS Pathogens

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

(2022) Matthew McCallum et al.   SCIENCE

Emergence and phenotypic characterization of the global SARS-CoV-2 C.1.2 lineage

(2022) Cathrine Scheepers et al.   Nature Communications

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

(2021) Tyler N. Starr et al.   SCIENCE

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

(2021) Emma C. Thomson et al.   CELL

An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants

(2021) Kui K. Chan et al.   Science Advances

Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies

(2021) Xing Zhu et al.   PLOS BIOLOGY

A human coronavirus evolves antigenically to escape antibody immunity

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

Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants

(2021) Charlie Laffeber et al.   JOURNAL OF MOLECULAR BIOLOGY

A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees

(2021) Jakob McBroome et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2021) Tyler N. Starr et al.   NATURE

High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape

(2021) Fabian Schmidt et al.   NATURE

The biological and clinical significance of emerging SARS-CoV-2 variants

(2021) Kaiming Tao et al.   NATURE REVIEWS GENETICS

Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants

(2021) Meng Yuan et al.   SCIENCE

Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies

(2021) Allison J. Greaney et al.   Nature Communications

Mutants of human ACE2 differentially promote SARS-CoV and SARS-CoV-2 spike mediated infection

(2021) Nidhi Shukla et al.   PLoS Pathogens

SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution

(2021) Jiří Zahradník et al.   Nature Microbiology

Rapid characterization of spike variants via mammalian cell surface display

(2021) Kamyab Javanmardi et al.   MOLECULAR CELL

The N501Y spike substitution enhances SARS-CoV-2 infection and transmission

(2021) Yang Liu et al.   NATURE

Conformational dynamics of the Beta and Kappa SARS-CoV-2 spike proteins and their complexes with ACE2 receptor revealed by cryo-EM

(2021) Yifan Wang et al.   Nature Communications

Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants

(2021) Pengcheng Han et al.   Nature Communications

High-titer neutralization of Mu and C.1.2 SARS-CoV-2 variants by vaccine-elicited antibodies of previously infected individuals

(2021) Takuya Tada et al.   Cell Reports

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

(2020) Jun Lan et al.   NATURE

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

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

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

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

The human coronavirus HCoV‐229E S‐protein structure and receptor binding

(2019) Zhijie Li et al.   eLife

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

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

Receptor-binding loops in alphacoronavirus adaptation and evolution

(2017) Alan H. M. Wong et al.   Nature Communications

Sort-seq under the hood: implications of design choices on large-scale characterization of sequence-function relations

(2016) Neil Peterman et al.   BMC GENOMICS

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves

(2016) Rhys M Adams et al.   eLife

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

fitdistrplus: AnRPackage for Fitting Distributions

(2015) Marie Laure Delignette-Muller et al.   Journal of Statistical Software

Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs

(2015) Michael B. Doud et al.   MOLECULAR BIOLOGY AND EVOLUTION

A human transcription factor in search mode

(2015) Kevin Hauser et al.   NUCLEIC ACIDS RESEARCH

REFMAC5 for the refinement of macromolecular crystal structures

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

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

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B