SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

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

(2020) Peng Zhou et al.   NATURE

Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence

(2020) Mayya Sedova et al.   BIOINFORMATICS

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

SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective

(2020) Manuela Sironi et al.   INFECTION GENETICS AND EVOLUTION

Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach

(2020) Lovika Mittal et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Evaluation of Nucleocapsid and Spike Protein-Based Enzyme-Linked Immunosorbent Assays for Detecting Antibodies against SARS-CoV-2

(2020) Wanbing Liu et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing

(2020) David E. Gordon et al.   NATURE

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

(2020) Zhenming Jin 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

Structure of the RNA-dependent RNA polymerase from COVID-19 virus

(2020) Yan Gao et al.   SCIENCE

Race to find COVID-19 treatments accelerates

(2020) Kai Kupferschmidt et al.   SCIENCE

A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping

(2020) Maria Romano et al.   Cells

COVID-19: Drug Targets and Potential Treatments

(2020) Carmen Gil et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular docking and simulation studies on SARS-CoV-2 Mpro reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19

(2020) Kiran Bharat Lokhande et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

DeepDDG: Predicting the Stability Change of Protein Point Mutations Using Neural Networks

(2019) Huali Cao et al.   Journal of Chemical Information and Modeling

Membrane binding proteins of coronaviruses

(2019) Entedar A J Alsaadi et al.   Future Virology

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation

(2019) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures

(2019) Antonina Andreeva et al.   NUCLEIC ACIDS RESEARCH

Disulfiram can inhibit MERS and SARS coronavirus papain-like proteases via different modes

(2018) Min-Han Lin et al.   ANTIVIRAL RESEARCH

ssbio: a Python framework for structural systems biology

(2018) Nathan Mih et al.   BIOINFORMATICS

Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem

(2018) Tomohiro Ban et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Data Sets Representative of the Structures and Experimental Properties of FDA-Approved Drugs

(2018) Dominique Douguet   ACS Medicinal Chemistry Letters

GenBank

(2018) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

CATH: expanding the horizons of structure-based functional annotations for genome sequences

(2018) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

GISAID: Global initiative on sharing all influenza data – from vision to reality

(2017) Yuelong Shu et al.   Eurosurveillance

The ClusPro web server for protein–protein docking

(2017) Dima Kozakov et al.   Nature Protocols

Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains

(2016) David R. Fidler et al.   TRAFFIC

Protease inhibitors targeting coronavirus and filovirus entry

(2015) Yanchen Zhou et al.   ANTIVIRAL RESEARCH

PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels

(2015) Yongwook Choi et al.   BIOINFORMATICS

MAESTRO - multi agent stability prediction upon point mutations

(2015) Josef Laimer et al.   BMC BIOINFORMATICS

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

Stock-based detection of protein oligomeric states in jsPISA

(2015) Eugene Krissinel   NUCLEIC ACIDS RESEARCH

Structural basis and functional analysis of the SARS coronavirus nsp14–nsp10 complex

(2015) Yuanyuan Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis

(2015) Bernardo Ochoa-Montaño et al.   Database-The Journal of Biological Databases and Curation

Accessory proteins of SARS-CoV and other coronaviruses

(2014) Ding Xiang Liu et al.   ANTIVIRAL RESEARCH

From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design

(2014) Rolf Hilgenfeld   FEBS Journal

Virus-host interactomics: new insights and opportunities for antiviral drug discovery

(2014) Benoît de Chassey et al.   Genome Medicine

SARS-CoV ORF1b-encoded nonstructural proteins 12–16: Replicative enzymes as antiviral targets

(2013) Lorenzo Subissi et al.   ANTIVIRAL RESEARCH

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Blocking eIF4E-eIF4G Interaction as a Strategy To Impair Coronavirus Replication

(2011) R. Cencic et al.   JOURNAL OF VIROLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The spike protein of SARS-CoV — a target for vaccine and therapeutic development

(2009) Lanying Du et al.   NATURE REVIEWS MICROBIOLOGY

Computational Validation of the Importance of Absolute Stereochemistry in Virtual Screening

(2008) Wesley H. Brooks et al.   Journal of Chemical Information and Modeling

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