Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography

Drug targeting Nsp1-ribosomal complex shows antiviral activity against SARS-CoV-2

(2022) Mohammad Afsar et al.   eLife

Nsp1 protein of SARS-CoV-2 disrupts the mRNA export machinery to inhibit host gene expression

(2021) Ke Zhang et al.   Science Advances

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

An oral SARS-CoV-2 M pro inhibitor clinical candidate for the treatment of COVID-19

(2021) Dafydd R. Owen et al.   SCIENCE

The N-terminal domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and preservation of viral gene expression

(2021) Aaron S. Mendez et al.   Cell Reports

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

(2020)   Nature Microbiology

The proximal origin of SARS-CoV-2

(2020) Kristian G. Andersen et al.   NATURE MEDICINE

Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2

(2020) Matthias Thoms et al.   SCIENCE

SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation

(2020) Katharina Schubert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SARS-CoV-2 nsp1: Bioinformatics, Potential Structural and Functional Features, and Implications for Drug/Vaccine Designs

(2020) Yuan-Qin Min et al.   Frontiers in Microbiology

Structure of nonstructural protein 1 from SARS-CoV-2.

(2020) Lauren K. Clark et al.   JOURNAL OF VIROLOGY

Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA

(2020) Shuai Yuan et al.   MOLECULAR CELL

The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation

(2020) Antonin TIDU et al.   RNA

A conserved region of nonstructural protein 1 from alphacoronaviruses inhibits host gene expression and is critical for viral virulence

(2019) Zhou Shen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

CDD/SPARCLE: the conserved domain database in 2020

(2019) Shennan Lu et al.   NUCLEIC ACIDS RESEARCH

Cryptic binding sites on proteins: definition, detection, and druggability

(2018) Sandor Vajda et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Exploring Cryptic Pockets Formation in Targets of Pharmaceutical Interest with SWISH

(2018) Federico Comitani et al.   Journal of Chemical Theory and Computation

RNA force field with accuracy comparable to state-of-the-art protein force fields

(2018) Dazhi Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Developing a molecular dynamics force field for both folded and disordered protein states

(2018) Paul Robustelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations

(2017) Gerard Martínez-Rosell et al.   Journal of Chemical Information and Modeling

Structural Basis for the Inhibition of Host Gene Expression by Porcine Epidemic Diarrhea Virus nsp1

(2017) Zhou Shen et al.   JOURNAL OF VIROLOGY

MERS coronavirus nsp1 participates in an efficient propagation through a specific interaction with viral RNA

(2017) Yutaka Terada et al.   VIROLOGY

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density

(2017) Nicholas M. Pearce et al.   Nature Communications

New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure

(2016) Maciej Antczak et al.   ACTA BIOCHIMICA POLONICA

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations

(2016) Vladimiras Oleinikovas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States

(2015) Stefano Piana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

(2015) Dima Kozakov et al.   Nature Protocols

PANDDAs: multi-dataset methods for finding hits from fragment screening by X-ray crystallography

(2015) Nicholas M. Pearce et al.   Acta Crystallographica A-Foundation and Advances

Rooting the Phylogenetic Tree of Middle East Respiratory Syndrome Coronavirus by Characterization of a Conspecific Virus from an African Bat

(2014) V. M. Corman et al.   JOURNAL OF VIROLOGY

DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment

(2012) A. Volkamer et al.   BIOINFORMATICS

Severe Acute Respiratory Syndrome Coronavirus nsp1 Facilitates Efficient Propagation in Cells through a Specific Translational Shutoff of Host mRNA

(2012) T. Tanaka et al.   JOURNAL OF VIROLOGY

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets

(2010) Goutam Mukherjee et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Coronavirus Genomics and Bioinformatics Analysis

(2010) Patrick C. Y. Woo et al.   Viruses-Basel

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Severe Acute Respiratory Syndrome Coronavirus nsp1 Suppresses Host Gene Expression, Including That of Type I Interferon, in Infected Cells

(2008) K. Narayanan et al.   JOURNAL OF VIROLOGY