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

SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential

(2021) Neha Vithani et al.   BIOPHYSICAL JOURNAL

The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

(2021) Jasmine Cubuk et al.   Nature Communications

Computational epitope map of SARS-CoV-2 spike protein

(2021) Mateusz Sikora et al.   PLoS Computational Biology

Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target

(2020) Haibo Zhang et al.   INTENSIVE CARE MEDICINE

The reproductive number of COVID-19 is higher compared to SARS coronavirus

(2020) Ying Liu et al.   JOURNAL OF TRAVEL MEDICINE

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

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

(2020) Daniel Wrapp et al.   SCIENCE

Coronavirus: covid-19 has killed more people than SARS and MERS combined, despite lower case fatality rate

(2020) Elisabeth Mahase   BMJ-British Medical Journal

The Cap-Snatching SFTSV Endonuclease Domain Is an Antiviral Target

(2020) Wenjie Wang et al.   Cell Reports

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

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

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

Structural basis of receptor recognition by SARS-CoV-2

(2020) Jian Shang 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

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

(2020) Linlin Zhang 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

Vulnerabilities in coronavirus glycan shields despite extensive glycosylation

(2020) Yasunori Watanabe et al.   Nature Communications

Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy

(2020) Bhupesh Goyal et al.   ACS Combinatorial Science

Conformational distributions of isolated myosin motor domains encode their mechanochemical properties

(2020) Justin R Porter et al.   eLife

Crowdsourcing drug discovery for pandemics

(2020) John Chodera et al.   Nature Chemistry

Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail

(2020) Johanna Hansen et al.   SCIENCE

Distinct conformational states of SARS-CoV-2 spike protein

(2020) Yongfei Cai et al.   SCIENCE

Linear epitopes of SARS-CoV-2 spike protein elicit neutralizing antibodies in COVID-19 patients

(2020) Yang Li et al.   Cellular & Molecular Immunology

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

(2020) Donald J. Benton 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

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

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

Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein

(2020) Dhurvas Chandrasekaran Dinesh et al.   PLoS Pathogens

Elucidating molecular mechanisms of functional conformational changes of proteins via Markov state models

(2020) Xiaowei Wang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Enspara: Modeling molecular ensembles with scalable data structures and parallel computing

(2019) J. R. Porter et al.   JOURNAL OF CHEMICAL PHYSICS

Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling

(2019) Justin R. Porter et al.   BIOPHYSICAL JOURNAL

Structure-Based Vaccine Antigen Design

(2019) Barney S. Graham et al.   Annual Review of Medicine

The dynamic conformational landscape of the protein methyltransferase SETD8

(2019) Shi Chen et al.   eLife

Coronavirus genomic RNA packaging

(2019) Paul S. Masters   VIROLOGY

Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly

(2018) Zhaoming Su et al.   CELL

Markov State Models: From an Art to a Science

(2018) Brooke E. Husic et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Choice of adaptive sampling strategy impacts state discovery, transition probabilities, and the apparent mechanism of conformational changes

(2018) Maxwell I. Zimmerman et al.   Journal of Chemical Theory and Computation

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

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

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities

(2018) Catherine R. Knoverek et al.   TRENDS IN BIOCHEMICAL SCIENCES

Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding

(2018) Xianqiang Sun et al.   eLife

Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains

(2017) Yuan Yuan et al.   Nature Communications

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models

(2017) Maxwell I. Zimmerman et al.   ACS Central Science

Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators

(2017) Kathryn M. Hart et al.   PLoS One

Modelling proteins’ hidden conformations to predict antibiotic resistance

(2016) Kathryn M. Hart et al.   Nature Communications

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs

(2015) Maxwell I. Zimmerman et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation

(2015) Gregory R. Bowman   JOURNAL OF COMPUTATIONAL CHEMISTRY

Molecular Docking and Structure-Based Drug Design Strategies

(2015) Leonardo Ferreira et al.   MOLECULES

The Coronavirus Nucleocapsid Is a Multifunctional Protein

(2014) Ruth McBride et al.   Viruses-Basel

Activation pathway of Src kinase reveals intermediate states as targets for drug design

(2014) Diwakar Shukla et al.   Nature Communications

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

(2013) Kai J. Kohlhoff et al.   Nature Chemistry

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Everything you wanted to know about Markov State Models but were afraid to ask

(2010) Vijay S. Pande et al.   METHODS

Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor

(2009) K. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation