Key Interacting Residues between RBD of SARS-CoV-2 and ACE2 Receptor: Combination of Molecular Dynamics Simulation and Density Functional Calculation

Rapid Development of SARS-CoV-2 Spike Protein Receptor-Binding Domain Self-Assembled Nanoparticle Vaccine Candidates

(2021) Yin-Feng Kang et al.   ACS Nano

A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein

(2021) Cheolmin Kim et al.   Nature Communications

SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice

(2021) Jing-Hui Tian et al.   Nature Communications

Comparison of the binding characteristics of SARS-CoV and SARS-CoV-2 RBDs to ACE2 at different temperatures by MD simulations

(2021) Fang-Fang Yan et al.   BRIEFINGS IN BIOINFORMATICS

Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera

(2021) Piyada Supasa et al.   CELL

BNT162b vaccines protect rhesus macaques from SARS-CoV-2

(2021) Annette B. Vogel 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

Human ACE2 peptide-mimics block SARS-CoV-2 pulmonary cells infection

(2021) Philippe Karoyan et al.   Communications Biology

Computational Mutagenesis at the SARS-CoV-2 Spike Protein/Angiotensin-Converting Enzyme 2 Binding Interface: Comparison with Experimental Evidence

(2021) Erik Laurini et al.   ACS Nano

Structural basis for the different states of the spike protein of SARS-CoV-2 in complex with ACE2

(2021) Renhong Yan et al.   CELL RESEARCH

Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Spike mutation T478K

(2021) Simone Di Giacomo et al.   JOURNAL OF MEDICAL VIROLOGY

Drugs that inhibit TMEM16 proteins block SARS-CoV-2 spike-induced syncytia

(2021) Luca Braga et al.   NATURE

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

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

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

Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein

(2020) Shuai Xia et al.   Cellular & Molecular Immunology

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

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

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

(2020) Daniel Wrapp 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

Computational Design of ACE2-Based Peptide Inhibitors of SARS-CoV-2

(2020) Yanxiao Han et al.   ACS Nano

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

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

Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atoms Simulations

(2020) Angelo Spinello et al.   Journal of Physical Chemistry Letters

Comparing the Binding Interactions in the Receptor Binding Domains of SARS-CoV-2 and SARS-CoV

(2020) Muhamed Amin et al.   Journal of Physical Chemistry Letters

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

(2020) Jun Lan et al.   NATURE

Structural basis of receptor recognition by SARS-CoV-2

(2020) Jian Shang et al.   NATURE

Developing Covid-19 Vaccines at Pandemic Speed

(2020) Nicole Lurie et al.   NEW ENGLAND JOURNAL OF MEDICINE

Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2

(2020) Jiahua He et al.   Viruses-Basel

Enhanced Binding of SARS-CoV-2 Spike Protein to Receptor by Distal Polybasic Cleavage Sites

(2020) Baofu Qiao et al.   ACS Nano

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

(2020) Tyler N. Starr et al.   CELL

Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies

(2020) Ivan Mercurio et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Airborne Transmission of SARS-CoV-2

(2020) Michael Klompas et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Computational Prediction of Mutational Effects on the SARS-CoV-2 Binding by Relative Free Energy Calculations

(2020) Junjie Zou et al.   Journal of Chemical Information and Modeling

Critical Differences between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV

(2020) Chen Bai et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Does SARS-CoV-2 Bind to Human ACE2 Stronger Than SARS-CoV?

(2020) Hoang Linh Nguyen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thermodynamic dissection of the intercalation binding process of doxorubicin to dsDNA with implications of ionic and solvent effects

(2020) Bahaa Jawad et al.   JOURNAL OF PHYSICAL CHEMISTRY B

COVID-19 vaccine development and a potential nanomaterial path forward

(2020) Matthew D. Shin et al.   Nature Nanotechnology

Accelerating Development of SARS-CoV-2 Vaccines — The Role for Controlled Human Infection Models

(2020) Meagan E. Deming et al.   NEW ENGLAND JOURNAL OF MEDICINE

An mRNA Vaccine against SARS-CoV-2 — Preliminary Report

(2020) Lisa A. Jackson et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

(2020) Kui K. Chan et al.   SCIENCE

Structure-based drug designing and immunoinformatics approach for SARS-CoV-2

(2020) Pritam Kumar Panda et al.   Science Advances

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

SARS-CoV-2 vaccines in development

(2020) Florian Krammer   NATURE

Computational Insights into the Conformational Accessibility and Binding Strength of SARS-CoV-2 Spike Protein to Human Angiotensin-Converting Enzyme 2

(2020) Cheng Peng et al.   Journal of Physical Chemistry Letters

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

Spike Proteins of SARS-CoV and SARS-CoV-2 Utilize Different Mechanisms to Bind With Human ACE2

(2020) Yixin Xie et al.   Frontiers in Molecular Biosciences

Coronavirus envelope protein: current knowledge

(2019) Dewald Schoeman et al.   Virology Journal

DelPhi Suite: New Developments and Review of Functionalities

(2019) Chuan Li et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation

(2018) Huan-Xiang Zhou et al.   CHEMICAL REVIEWS

Impact of Hydrogen Bonding in the Binding Site between Capsid Protein and MS2 Bacteriophage ssRNA

(2017) Lokendra Poudel et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Implication of the solvent effect, metal ions and topology in the electronic structure and hydrogen bonding of human telomeric G-quadruplex DNA

(2016) Lokendra Poudel et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Electronic Structure, Dielectric Response and Surface Charge Distribution of RGD (1FUV) Peptide

(2014) Puja Adhikari et al.   Scientific Reports

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method

(2012) Nadine Homeyer et al.   Molecular Informatics

DelPhi: a comprehensive suite for DelPhi software and associated resources

(2012) Lin Li et al.   BMC Biophysics

Ab initioinvestigation of hydrogen bonding and network structure in a supercooled model of water

(2011) Lei Liang et al.   PHYSICAL REVIEW B

Definition of the hydrogen bond (IUPAC Recommendations 2011)

(2011) Elangannan Arunan et al.   PURE AND APPLIED CHEMISTRY

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE