Atomistic Simulations and In Silico Mutational Profiling of Protein Stability and Binding in the SARS-CoV-2 Spike Protein Complexes with Nanobodies: Molecular Determinants of Mutational Escape Mechanisms

Dynamic Network Modeling of Allosteric Interactions and Communication Pathways in the SARS-CoV-2 Spike Trimer Mutants: Differential Modulation of Conformational Landscapes and Signal Transmission via Cascades of Regulatory Switches

(2021) Gennady M. Verkhivker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

First detection of SARS-CoV-2 spike protein N501 mutation in Italy in August, 2020

(2021) Simona Fiorentini et al.   LANCET INFECTIOUS DISEASES

Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape

(2021) Paul-Albert Koenig et al.   SCIENCE

Structural Analysis of Neutralizing Epitopes of the SARS-CoV-2 Spike to Guide Therapy and Vaccine Design Strategies

(2021) Maxwell T. Finkelstein et al.   Viruses-Basel

Binding Revisited—Avidity in Cellular Function and Signaling

(2021) Simon Erlendsson et al.   Frontiers in Molecular Biosciences

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

Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

(2021) Carolina M. Voloch et al.   JOURNAL OF VIROLOGY

Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence

(2021) Ester C Sabino et al.   LANCET

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

(2021) Houriiyah Tegally et al.   NATURE

Sixteen novel lineages of SARS-CoV-2 in South Africa

(2021) Houriiyah Tegally et al.   NATURE MEDICINE

Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies: Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations

(2021) Gennady M. Verkhivker et al.   BIOCHEMISTRY

Critical Interactions Between the SARS-CoV-2 Spike Glycoprotein and the Human ACE2 Receptor

(2021) Elhan Taka et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Integrated Biophysical Modeling of the SARS-CoV-2 Spike Protein Binding and Allosteric Interactions with Antibodies

(2021) Gennady M. Verkhivker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2021) Nicholas G. Davies et al.   NATURE

Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

(2021) Erik Volz et al.   NATURE

Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies

(2021) Delphine Planas et al.   NATURE MEDICINE

Cross-Reactive Neutralizing Antibody Responses Elicited by SARS-CoV-2 501Y.V2 (B.1.351)

(2021) Thandeka Moyo-Gwete et al.   NEW ENGLAND JOURNAL OF MEDICINE

Preparing for the Future — Nanobodies for Covid-19?

(2021) Ram Sasisekharan   NEW ENGLAND JOURNAL OF MEDICINE

Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice

(2021) Phillip Pymm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational epitope map of SARS-CoV-2 spike protein

(2021) Mateusz Sikora et al.   PLoS Computational Biology

Neutralization of SARS‐CoV‐2 by highly potent, hyperthermostable, and mutation‐tolerant nanobodies

(2021) Thomas Güttler et al.   EMBO JOURNAL

Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021

(2021) Finlay Campbell et al.   Eurosurveillance

Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveals the Allosteric Duality of Functionally Adaptable Hotspots

(2021) Gennady Verkhivker et al.   Journal of Chemical Theory and Computation

In vivo monoclonal antibody efficacy against SARS-CoV-2 variant strains

(2021) Rita E. Chen et al.   NATURE

Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants

(2021) Jianliang Xu et al.   NATURE

A glycan gate controls opening of the SARS-CoV-2 spike protein

(2021) Terra Sztain et al.   Nature Chemistry

SARS-CoV-2 variants, spike mutations and immune escape

(2021) William T. Harvey et al.   NATURE REVIEWS MICROBIOLOGY

SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma

(2021) Emanuele Andreano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes

(2021) Dapeng Sun et al.   Nature Communications

One-shot identification of SARS-CoV-2 S RBD escape mutants using yeast screening

(2021) Irene M. Francino-Urdaniz et al.   Cell Reports

Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS

(2020) Yushun Wan et al.   JOURNAL OF VIROLOGY

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

(2020) Daniel Wrapp et al.   SCIENCE

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2

(2020) Qihui Wang et al.   CELL

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

(2020) Alexandra C. Walls et al.   CELL

Characterization of the receptor-binding domain (RBD) of 2019 novel coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine

(2020) Wanbo Tai et al.   Cellular & Molecular Immunology

Key residues of the receptor binding motif in the spike protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies

(2020) Chunyan Yi et al.   Cellular & Molecular Immunology

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

(2020) Rui Shi et al.   NATURE

Human neutralizing antibodies elicited by SARS-CoV-2 infection

(2020) Bin Ju et al.   NATURE

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

(2020) Dora Pinto et al.   NATURE

A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2

(2020) Yan Wu et al.   SCIENCE

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

A human monoclonal antibody blocking SARS-CoV-2 infection

(2020) Chunyan Wang et al.   Nature Communications

Vulnerabilities in coronavirus glycan shields despite extensive glycosylation

(2020) Yasunori Watanabe et al.   Nature Communications

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

(2020) Tyler N. Starr et al.   CELL

Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

(2020) Jiandong Huo et al.   Cell Host & Microbe

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

Controlling the SARS-CoV-2 spike glycoprotein conformation

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

A thermostable, closed SARS-CoV-2 spike protein trimer

(2020) Xiaoli Xiong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation

(2020) Matthew McCallum et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Neutralizing nanobodies bind SARS-CoV-2 spike RBD and block interaction with ACE2

(2020) Jiangdong Huo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2

(2020) Xiangyang Chi et al.   SCIENCE

Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies

(2020) Alina Baum et al.   SCIENCE

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

Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody

(2020) Zhe Lv et al.   SCIENCE

Distinct conformational states of SARS-CoV-2 spike protein

(2020) Yongfei Cai et al.   SCIENCE

Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability

(2020) Philip J. M. Brouwer et al.   SCIENCE

Cryo-EM analysis of the post-fusion structure of the SARS-CoV spike glycoprotein

(2020) Xiaoyi Fan et al.   Nature Communications

Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy

(2020) Shuo Du et al.   CELL

Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states

(2020) Mert Gur et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Spike Proteins

(2020) Gennady M. Verkhivker   JOURNAL OF PROTEOME RESEARCH

Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion

(2020) Donald J. Benton et al.   NATURE

SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies

(2020) Christopher O. Barnes et al.   NATURE

Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2

(2020) Colton J. Bracken et al.   Nature Chemical Biology

Functional plasticity and evolutionary adaptation of allosteric regulation

(2020) Megan Leander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2020) Beata Turoňová et al.   SCIENCE

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

(2020) M. Alejandra Tortorici et al.   SCIENCE

Structural Basis of SARS-CoV-2 and SARS-CoV Antibody Interactions

(2020) Edem Gavor et al.   TRENDS IN IMMUNOLOGY

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein

(2020) Lorenzo Casalino et al.   ACS Central Science

Fighting COVID-19 Using Molecular Dynamics Simulations

(2020) Pablo R. Arantes et al.   ACS Central Science

Real-Time Conformational Dynamics of SARS-CoV-2 Spikes on Virus Particles

(2020) Maolin Lu et al.   Cell Host & Microbe

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

Assessment of software methods for estimating protein-protein relative binding affinities

(2020) Tawny R. Gonzalez et al.   PLoS One

Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM

(2020) Cong Xu et al.   Science Advances

A multiscale coarse-grained model of the SARS-CoV-2 virion

(2020) Alvin Yu et al.   BIOPHYSICAL JOURNAL

Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1

(2019) Tal Einav et al.   Cell Systems

BindProfX: Assessing Mutation-Induced Binding Affinity Change by Protein Interface Profiles with Pseudo-Counts

(2017) Peng Xiong et al.   JOURNAL OF MOLECULAR BIOLOGY

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion

(2017) Alexandra C. Walls et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

3Drefine: an interactive web server for efficient protein structure refinement

(2016) Debswapna Bhattacharya et al.   NUCLEIC ACIDS RESEARCH

OUP accepted manuscript

(2016)   NUCLEIC ACIDS RESEARCH

The anisotropic network model web server at 2015 (ANM 2.0)

(2015) E. Eyal et al.   BIOINFORMATICS

A Stochastic Algorithm for the Isobaric–Isothermal Ensemble with Ewald Summations for All Long Range Forces

(2015) Michele Di Pierro et al.   Journal of Chemical Theory and Computation

Avidity and positive allosteric modulation/cooperativity act hand in hand to increase the residence time of bivalent receptor ligands

(2013) Georges Vauquelin et al.   FUNDAMENTAL & CLINICAL PHARMACOLOGY

Stability Mechanisms of Laccase Isoforms using a Modified FoldX Protocol Applicable to Widely Different Proteins

(2013) Niels J. Christensen et al.   Journal of Chemical Theory and Computation

Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories

(2013) Panagiotis I. Koukos et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

(2013) Yves Dehouck et al.   NUCLEIC ACIDS RESEARCH

Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol

(2012) Niels J. Christensen et al.   Journal of Chemical Information and Modeling

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

A graphical interface for the FoldX forcefield

(2011) J. Van Durme et al.   BIOINFORMATICS

Global Dynamics of Proteins: Bridging Between Structure and Function

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

WIWS: a protein structure bioinformatics Web service collection

(2010) M. L. Hekkelman et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS