Analyzing the effect of mutations in SARS-CoV2 papain-like protease from Saudi isolates on protein structure and drug-protein binding: Molecular modelling and dynamics studies

Mutations in SARS‐CoV‐2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure

(2021) Shamlan M. S. Reshamwala et al.   JOURNAL OF MEDICAL VIROLOGY

The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery

(2021) Ziyang Fu et al.   Nature Communications

SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity

(2021) Seiya Ozono et al.   Nature Communications

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors

(2021) Jerzy Osipiuk et al.   Nature Communications

Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China

(2020) Aiping Wu et al.   Cell Host & Microbe

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

Comparing the Binding Interactions in the Receptor Binding Domains of SARS-CoV-2 and SARS-CoV

(2020) Muhamed Amin et al.   Journal of Physical Chemistry Letters

Characterization and noncovalent inhibition of the deubiquitinase and deISGylase activity of SARS-CoV-2 papain-like protease

(2020) Brendan T Freitas et al.   ACS Infectious Diseases

Variant analysis of SARS-CoV-2 genomes

(2020) Takahiko Koyama et al.   BULLETIN OF THE WORLD HEALTH ORGANIZATION

Mutations Strengthened SARS-CoV-2 Infectivity

(2020) Jiahui Chen et al.   JOURNAL OF MOLECULAR BIOLOGY

Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity

(2020) Donghyuk Shin et al.   NATURE

Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy

(2020) Hongjing Gu et al.   SCIENCE

Structure-based virtual screening and molecular dynamics of phytochemicals derived from Saudi medicinal plants to identify potential COVID-19 therapeutics

(2020) Mubarak A. Alamri et al.   Arabian Journal of Chemistry

Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure

(2020) Gyanendra Bahadur Chand et al.   PeerJ

Insights Into Dynamics of Inhibitor and Ubiquitin-Like Protein Binding in SARS-CoV-2 Papain-Like Protease

(2020) Yuliana K. Bosken et al.   Frontiers in Molecular Biosciences

Spike mutation D614G alters SARS-CoV-2 fitness

(2020) Jessica A. Plante et al.   NATURE

Temporal signal and the phylodynamic threshold of SARS-CoV-2

(2020) Sebastian Duchene et al.   Virus Evolution

Key genetic elements, single and in clusters, underlying geographically dependent SARS-CoV-2 genetic adaptation and their impact on binding affinity for drugs and immune control

(2020) Romina Salpini et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

(2018) Carlos HM Rodrigues et al.   NUCLEIC ACIDS RESEARCH

Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species

(2017) Courtney M. Daczkowski et al.   JOURNAL OF MOLECULAR BIOLOGY

Accessory proteins of SARS-CoV and other coronaviruses

(2014) Ding Xiang Liu et al.   ANTIVIRAL RESEARCH

X-ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-like Proteases

(2014) Yahira M. Báez-Santos et al.   JOURNAL OF MEDICINAL CHEMISTRY

The SARS coronavirus papain like protease can inhibit IRF3 at a post activation step that requires deubiquitination activity

(2014) Krystal Matthews et al.   Virology Journal

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

(2014) Vincent Frappier et al.   PLoS Computational Biology

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes

(2013) Romain A. Studer et al.   BIOCHEMICAL JOURNAL

SwissParam: A fast force field generation tool for small organic molecules

(2011) Vincent Zoete et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Severe Acute Respiratory Syndrome Coronavirus Papain-like Novel Protease Inhibitors: Design, Synthesis, Protein−Ligand X-ray Structure and Biological Evaluation

(2010) Arun K. Ghosh et al.   JOURNAL OF MEDICINAL CHEMISTRY

Radius of gyration as an indicator of protein structure compactness

(2008) M. Yu. Lobanov et al.   MOLECULAR BIOLOGY

A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication

(2008) K. Ratia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA