Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism

Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants

(2022) James W. Saville et al.   Nature Communications

Insights into Binding of Single-Stranded Viral RNA Template to the Replication–Transcription Complex of SARS-CoV-2 for the Priming Reaction from Molecular Dynamics Simulations

(2022) Jimin Wang et al.   BIOCHEMISTRY

Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme

(2022) Jimin Wang et al.   BIOCHEMISTRY

Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain

(2022) Gang Ye et al.   Nature Communications

Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike

(2022) Marco A Díaz-Salinas et al.   eLife

Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV-2

(2022) Jimin Wang et al.   BIOCHEMISTRY

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM

(2022) Jimin Wang et al.   JOURNAL OF STRUCTURAL BIOLOGY

A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening

(2021) Christoph Gorgulla et al.   iScience

SARS-CoV-2 spike protein stabilized in the closed state induces potent neutralizing responses.

(2021) George W. Carnell et al.   JOURNAL OF VIROLOGY

Sodium-glucose co-transporter inhibitors in insulin-treated diabetes: a meta-analysis

(2021) João Pedro Ferreira et al.   EUROPEAN JOURNAL OF ENDOCRINOLOGY

SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

(2021) Maxwell I. Zimmerman et al.   Nature Chemistry

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

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

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS

(2021) Mario S. Valdés-Tresanco et al.   Journal of Chemical Theory and Computation

SARS-CoV-2 spreads through cell-to-cell transmission

(2021) Cong Zeng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding

(2021) Dhiraj Mannar et al.   Cell Reports

Scalable molecular dynamics on CPU and GPU architectures with NAMD

(2020) James C. Phillips et al.   JOURNAL OF CHEMICAL PHYSICS

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

Antibody signature induced by SARS-CoV-2 spike protein immunogens in rabbits

(2020) Supriya Ravichandran et al.   Science Translational Medicine

Unlocking COVID therapeutic targets: a structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike

(2020) João Trigueiro-Louro et al.   Computational and Structural Biotechnology Journal

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

(2020) Zunlong Ke et al.   NATURE

Free fatty acid binding pocket in the locked structure of SARS-CoV-2 spike protein

(2020) Christine Toelzer et al.   SCIENCE

Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2

(2020) Anamika Basu 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

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

(2020) Alexandra C. Walls et al.   CELL

Generalized Born Implicit Solvent Models for Biomolecules

(2019) Alexey V. Onufriev et al.   Annual Review of Biophysics

Valproic acid interactions with the NavMs voltage-gated sodium channel

(2019) Geancarlo Zanatta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Binding site for coenzyme A revealed in the structure of pyruvate:ferredoxin oxidoreductase fromMoorella thermoacetica

(2018) Percival Yang-Ting Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural insights into the π-π-π stacking mechanism and DNA-binding activity of the YEATS domain

(2018) Brianna J. Klein et al.   Nature Communications

Pre-fusion structure of a human coronavirus spike protein

(2016) Robert N. Kirchdoerfer et al.   NATURE

CHARMM36m: an improved force field for folded and intrinsically disordered proteins

(2016) Jing Huang et al.   NATURE METHODS

Structure, Function, and Evolution of Coronavirus Spike Proteins

(2016) Fang Li   Annual Review of Virology

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field

(2012) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

An improved generalized AMBER force field (GAFF) for urea

(2010) Gül Altınbaş Özpınar et al.   JOURNAL OF MOLECULAR MODELING

Sodium valproate: an old drug with new roles

(2009) Natalia N. Nalivaeva et al.   TRENDS IN PHARMACOLOGICAL SCIENCES