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

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

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

(2021) Tyler N. Starr 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

Antibody neutralization of SARS-CoV-2 through ACE2 receptor mimicry

(2021) Jiwan Ge et al.   Nature Communications

Molecular determinants and mechanism for antibody cocktail preventing SARS-CoV-2 escape

(2021) Zhiqiang Ku et al.   Nature Communications

The antigenic anatomy of SARS-CoV-2 receptor binding domain

(2021) Wanwisa Dejnirattisai 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

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

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

(2021) Pengfei 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

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

Enhanced binding of the N501Y‐mutated SARS‐CoV‐2 spike protein to the human ACE2 receptor: insights from molecular dynamics simulations

(2021) Binquan Luan et al.   FEBS LETTERS

Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease

(2021) Terra Sztain et al.   Journal of Chemical Information and Modeling

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

Computational epitope map of SARS-CoV-2 spike protein

(2021) Mateusz Sikora et al.   PLoS Computational Biology

The SARS-CoV-2 Spike variant D614G favors an open conformational state

(2021) Rachael A. Mansbach et al.   Science Advances

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 Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies

(2020) Daniel Wrapp et al.   CELL

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

(2020) Alexandra C. Walls et al.   CELL

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

Perturb–Scan–Pull: A Novel Method Facilitating Conformational Transitions in Proteins

(2020) Farzaneh Jalalypour et al.   Journal of Chemical Theory and Computation

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

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

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

(2020) Yan Wu 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

The SARS-CoV-2 Exerts a Distinctive Strategy for Interacting with the ACE2 Human Receptor

(2020) Esther S. Brielle 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

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

(2020) Qianqian Li 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

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

The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach

(2020) Luisa Di Paola et al.   JOURNAL OF PROTEOME RESEARCH

Controlling the SARS-CoV-2 spike glycoprotein conformation

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

Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient

(2020) Daming Zhou et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions

(2020) Yingjie Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2

(2020) Kui K. Chan 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

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

(2020) Meng Yuan et al.   SCIENCE

Fruitful neutralizing antibody pipeline brings hope to defeat SARS-Cov-2

(2020) Alex Renn et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Computational Alanine Scanning and Structural Analysis of the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Complex

(2020) Erik Laurini et al.   ACS Nano

A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model

(2020) Jakob Kreye et al.   CELL

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

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

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

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

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

Dynamics of the ACE2–SARS-CoV-2/SARS-CoV spike protein interface reveal unique mechanisms

(2020) Amanat Ali et al.   Scientific Reports

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

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

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

Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior

(2019) Yan Zhang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Dissecting Structure-Encoded Determinants of Allosteric Cross-Talk between Post-Translational Modification Sites in the Hsp90 Chaperones

(2018) Gabrielle Stetz et al.   Scientific Reports

Stabilized coronavirus spikes are resistant to conformational changes induced by receptor recognition or proteolysis

(2018) Robert N. Kirchdoerfer et al.   Scientific Reports

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

Adaptability of protein structures to enable functional interactions and evolutionary implications

(2015) Turkan Haliloglu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Cooperative Dynamics of Intact AMPA and NMDA Glutamate Receptors: Similarities and Subfamily-Specific Differences

(2015) Anindita Dutta et al.   STRUCTURE

ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones

(2014) Ignacio J. General et al.   PLoS Computational Biology

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

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

The FALC-Loop web server for protein loop modeling

(2011) J. Ko et al.   NUCLEIC ACIDS RESEARCH

Manipulation of Conformational Change in Proteins by Single-Residue Perturbations

(2010) C. Atilgan et al.   BIOPHYSICAL JOURNAL

WIWS: a protein structure bioinformatics Web service collection

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

Improved prediction of protein side-chain conformations with SCWRL4

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

Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein

(2009) Canan Atilgan et al.   PLoS Computational Biology