Analysis of natural compounds against the activity of SARS-CoV-2 NSP15 protein towards an effective treatment against COVID-19: a theoretical and computational biology approach

Novel Wuhan (2019-nCoV) Coronavirus

(2020) W. Graham Carlos et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

First cases of coronavirus disease 2019 (COVID-19) in the WHO European Region, 24 January to 21 February 2020

(2020) Gianfranco Spiteri et al.   Eurosurveillance

First Case of 2019 Novel Coronavirus in the United States

(2020) Michelle L. Holshue et al.   NEW ENGLAND JOURNAL OF MEDICINE

COVID-19 Outbreak: An Overview

(2020) Marco Ciotti et al.   CHEMOTHERAPY

Identification of Potential Inhibitors of SARS-COV-2 Endoribonuclease (EndoU) from FDA Approved Drugs: A Drug Repurposing Approach to find Therapeutics for COID19

(2020) Anshuman Chandra et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment

(2020) Subramanian Boopathi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV ‐2

(2020) Youngchang Kim et al.   PROTEIN SCIENCE

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

(2020) Yan Gao et al.   SCIENCE

Coronavirus disease 2019 (COVID-19): A literature review

(2020) Harapan Harapan et al.   Journal of Infection and Public Health

Virtual screening, pharmacokinetics, molecular dynamics and binding free energy analysis for small natural molecules against cyclin-dependent kinase 5 for Alzheimer’s disease

(2019) Rohit Shukla et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties

(2018) Hongbin Yang et al.   BIOINFORMATICS

Coronavirus nonstructural protein 15 mediates evasion of dsRNA sensors and limits apoptosis in macrophages

(2017) Xufang Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The anticancer agent 3-bromopyruvate: a simple but powerful molecule taken from the lab to the bedside

(2016) J. Azevedo-Silva et al.   JOURNAL OF BIOENERGETICS AND BIOMEMBRANES

Pre-fusion structure of a human coronavirus spike protein

(2016) Robert N. Kirchdoerfer et al.   NATURE

The SARS-coronavirus papain-like protease: Structure, function and inhibition by designed antiviral compounds

(2015) Yahira M. Báez-Santos et al.   ANTIVIRAL RESEARCH

ZINC 15 – Ligand Discovery for Everyone

(2015) Teague Sterling et al.   Journal of Chemical Information and Modeling

New ways to boost molecular dynamics simulations

(2015) Elmar Krieger et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

YASARA View—molecular graphics for all devices—from smartphones to workstations

(2014) Elmar Krieger et al.   BIOINFORMATICS

Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Insight into the Effect of Inhibitor Resistant S130G Mutant on Physico-Chemical Properties of SHV Type Beta-Lactamase: A Molecular Dynamics Study

(2014) Mohd Hassan Baig et al.   PLoS One

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

(2013) Lorenzo Subissi et al.   ANTIVIRAL RESEARCH

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

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

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties

(2012) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Biological effects of propionic acid in humans; metabolism, potential applications and underlying mechanisms

(2010) Sa'ad H. Al-Lahham et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Energetic Decomposition with the Generalized-Born and Poisson−Boltzmann Solvent Models: Lessons from Association of G-Protein Components

(2010) Noel Carrascal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How accurate are continuum solvation models for drug-like molecules?

(2009) Jacob Kongsted et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8

(2009) Elmar Krieger et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Radius of gyration as an indicator of protein structure compactness

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