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

Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2

(2020) Renhong Yan et al.   SCIENCE

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

(2020) Daniel Wrapp et al.   SCIENCE

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

(2020) Alexandra C. Walls et al.   CELL

A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19

(2020) Rommie E. Amaro et al.   Journal of Chemical Information and Modeling

Structure of replicating SARS-CoV-2 polymerase

(2020) Hauke S. Hillen et al.   NATURE

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

Site-specific glycan analysis of the SARS-CoV-2 spike

(2020) Yasunori Watanabe et al.   SCIENCE

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

(2020) Linlin Zhang et al.   SCIENCE

Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins

(2020) Suhas Srinivasan et al.   Viruses-Basel

TRIM5α self-assembly and compartmentalization of the HIV-1 viral capsid

(2020) Alvin Yu et al.   Nature Communications

SARS-CoV-2 (COVID-19) by the numbers

(2020) Yinon M Bar-On et al.   eLife

Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites

(2020) Sisi Kang et al.   Acta Pharmaceutica Sinica B

Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3

(2020) David N. Frick et al.   BIOCHEMISTRY

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

Distinct conformational states of SARS-CoV-2 spike protein

(2020) Yongfei Cai et al.   SCIENCE

Molecular Architecture of the SARS-CoV-2 Virus

(2020) Hangping Yao et al.   CELL

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

(2020) Zunlong Ke et al.   NATURE

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

(2020) Beata Turoňová et al.   SCIENCE

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

(2020) Lorenzo Casalino et al.   ACS Central Science

Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6)

(2020) Alvin Yu et al.   Science Advances

Multi-Configurational Coarse-Grained Molecular Dynamics.

(2019) Morris E. Sharp et al.   Journal of Chemical Theory and Computation

Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites

(2019) Alexander J. Pak et al.   Journal of Chemical Theory and Computation

Membrane Lipid Composition: Effect on Membrane and Organelle Structure, Function and Compartmentalization and Therapeutic Avenues

(2019) Doralicia Casares et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Coronavirus envelope protein: current knowledge

(2019) Dewald Schoeman et al.   Virology Journal

Off-Pathway Assembly: A Broad-Spectrum Mechanism of Action for Drugs That Undermine Controlled HIV-1 Viral Capsid Formation

(2019) Alexander J. Pak et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural model of the SARS coronavirus E channel in LMPG micelles

(2018) Wahyu Surya et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Neurotransmitter Funneling Optimizes Glutamate Receptor Kinetics

(2018) Alvin Yu et al.   NEURON

Glutamate and Glycine Binding to the NMDA Receptor

(2018) Alvin Yu et al.   STRUCTURE

Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments

(2018) Harshwardhan H. Katkar et al.   BIOPHYSICAL JOURNAL

Energetics of Glutamate Binding to an Ionotropic Glutamate Receptor

(2017) Alvin Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2016) Jing Huang et al.   NATURE METHODS

Molecular lock regulates binding of glycine to a primitive NMDA receptor

(2016) Alvin Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coarse-grained simulation reveals key features of HIV-1 capsid self-assembly

(2016) John M. A. Grime et al.   Nature Communications

JPred4: a protein secondary structure prediction server

(2015) Alexey Drozdetskiy et al.   NUCLEIC ACIDS RESEARCH

The SARS coronavirus nucleocapsid protein – Forms and functions

(2014) Chung-ke Chang et al.   ANTIVIRAL RESEARCH

The Theory of Ultra-Coarse-Graining. 2. Numerical Implementation

(2014) Aram Davtyan et al.   Journal of Chemical Theory and Computation

On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

(2013) Lin Li et al.   Journal of Chemical Theory and Computation

The Theory of Ultra-Coarse-Graining. 1. General Principles

(2013) James F. Dama et al.   Journal of Chemical Theory and Computation

Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs

(2013) Ron O. Dror et al.   NATURE

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

Coarse-graining errors and numerical optimization using a relative entropy framework

(2011) Aviel Chaimovich et al.   JOURNAL OF CHEMICAL PHYSICS

Improved prediction of protein side-chain conformations with SCWRL4

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

Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins

(2008) Edward Lyman et al.   BIOPHYSICAL JOURNAL

A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules

(2008) Zhiyong Zhang et al.   BIOPHYSICAL JOURNAL

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

(2008) W. G. Noid et al.   JOURNAL OF CHEMICAL PHYSICS

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The M, E, and N Structural Proteins of the Severe Acute Respiratory Syndrome Coronavirus Are Required for Efficient Assembly, Trafficking, and Release of Virus-Like Particles

(2008) Y. L. Siu et al.   JOURNAL OF VIROLOGY

Membrane lipids: where they are and how they behave

(2008) Gerrit van Meer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY