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EPIMED LAB METHODS BOOK

Laboratory Methods

Optimised Laboratory Methods Edition 3
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COVID-19 RELATED PUBLICATIONS

Utilization of the EpiMed Coronabank Chemical Collection to identify potential SARS-CoV-2 antivirals: in silico studies targeting the nsp14 ExoN domain and PLpro naphthalene binding site

A repository of COVID-19 related molecular dynamics simulations and utilisation in the context of nsp10-nsp16 antivirals

EpiMed Coronabank Chemical Collection: Compound selection, ADMET analysis, and utilisation in the context of potential SARS-CoV-2 antivirals

Chronicling the 3-year evolution of the COVID-19 pandemic: analysis of disease management, characteristics of major variants, and impacts on pathogenicity

Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain

The SARS-CoV-2 helicase as a target for antiviral therapy: Identification of potential small molecule inhibitors by in silico modelling

Small molecule interactions with the SARS-CoV-2 main protease: In silico all-atom microsecond MD simulations, PELE Monte Carlo simulations, and determination of in vitro activity inhibition

Investigation of small molecule inhibitors of the SARS-CoV-2 papain-like protease by all-atom microsecond modelling, PELE Monte Carlo simulations, and in vitro activity inhibition

In silico investigation to identify potential small molecule inhibitors of the RNA-dependent RNA polymerase (RdRp) nidovirus RdRp-associated nucleotidyltransferase domain

In silico investigation of potential small molecule inhibitors of the SARS-CoV-2 nsp10-nsp16 methyltransferase complex

Inhibition of interferon-stimulated gene 15 and lysine 48-linked ubiquitin binding to the SARS-CoV-2 papain-like protease by small molecules: In silico studies

Interaction of small molecules with the SARS-CoV-2 papain-like protease: In silico studies and in vitro validation of protease activity inhibition using an enzymatic inhibition assay

Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay

Site mapping and small molecule blind docking reveal a possible target site on the SARS-CoV-2 main protease dimer interface

Interaction of the prototypical α-ketoamide inhibitor with the SARS-CoV-2 main protease active site in silico: Molecular dynamic simulations highlight the stability of the ligand-protein complex

TRUSTED EXTERNAL RESOURCES

Pawsey Supercomputing Centre

Supercomputing Resources
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National Computing Infrastructure (NCI)

Supercomputing Resources
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Melbourne University High Performance Computing (Spartan)

Supercomputing Resources
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Hypernet Labs (Galileo computing)

Supercomputing Resources
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Australian Synchrotron

Synchrotron Science
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Automated Topology Builder and Repository

Molecular force fields for molecules
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DE SHAW Research

Long molecular dynamics simulations related to SARS-CoV-2
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Nextstrain

Coronavirus mutation tracker
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OliveNet Library

Small molecules associated with Olea Europaea
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Johns Hopkins University

Coronavirus resource centre
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World Health Organization

Coronavirus disease
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Centers for Disease Control and Prevention (CDC)

Coronavirus information
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National Institutes of Health (NIH)

Coronavirus information
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Science Magazine

Coronavirus collection
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Nature

Coronavirus collection
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