Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro

Recent discovery and development of inhibitors targeting coronaviruses

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A new coronavirus associated with human respiratory disease in China

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

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A Novel Coronavirus from Patients with Pneumonia in China, 2019

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Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission

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Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods

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Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study

(2020) Junmei Wang   Journal of Chemical Information and Modeling

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

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Delayed Initiation of Remdesivir in a COVID‐19‐Positive Patient

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Remdesivir for severe acute respiratory syndrome coronavirus 2 causing COVID-19: An evaluation of the evidence

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Structural elucidation of SARS-CoV-2 vital proteins: Computational methods reveal potential drug candidates against main protease, Nsp12 polymerase and Nsp13 helicase

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Computational screening of medicinal plant phytochemicals to discover potent pan-serotype inhibitors against dengue virus

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OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules

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Towards more effective acetylcholinesterase inhibitors: a comprehensive modelling study based on human acetylcholinesterase protein–drug complex

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Mutagenesis of DsbAss is Crucial for the Signal Recognition Particle Mechanism in Escherichia coli: Insights from Molecular Dynamics Simulations

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Deleterious Variants in WNT10A, EDAR, and EDA Causing Isolated and Syndromic Tooth Agenesis: A Structural Perspective from Molecular Dynamics Simulations

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Beyond cysteine: recent developments in the area of targeted covalent inhibition

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Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element

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Investigating the molecular mechanism of staphylococcal DNA gyrase inhibitors: A combined ligand-based and structure-based resources pipeline

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Discovery of selective inhibitors for cyclic AMP response element-binding protein

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An integrated approach towards the development of novel antifungal agents containing thiadiazole: synthesis and a combined similarity search, homology modelling, molecular dynamics and molecular docking study

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Perspectives towards antiviral drug discovery against Ebola virus

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Origin and evolution of pathogenic coronaviruses

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Antigenic Peptide Prediction From E6 and E7 Oncoproteins of HPV Types 16 and 18 for Therapeutic Vaccine Design Using Immunoinformatics and MD Simulation Analysis

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Covalent inhibitors design and discovery

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Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations

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Medicinal plant phytochemicals and their inhibitory activities against pancreatic lipase: molecular docking combined with molecular dynamics simulation approach

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Integrated Computational Approach for Virtual Hit Identification against Ebola Viral Proteins VP35 and VP40

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Discovery of Novel Dengue NS2B/NS3 Protease Inhibitors Using Pharmacophore Modeling and Molecular Docking Based Virtual Screening of the ZINC Database

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An Overview of Severe Acute Respiratory Syndrome–Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy

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MPD3: a useful medicinal plants database for drug designing

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Coronaviruses — drug discovery and therapeutic options

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Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking

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Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

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New direct-acting antivirals in hepatitis C therapy: a review of sofosbuvir, ledipasvir, daclatasvir, simeprevir, paritaprevir, ombitasvir and dasabuvir

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Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins

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The cysteine proteome

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The basics of thiols and cysteines in redox biology and chemistry

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Structure-Based Virtual Screening Approach for Discovery of Covalently Bound Ligands

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Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring

(2014) Kai Zhu et al.   Journal of Chemical Information and Modeling

A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring

(2014) Sarah Sirin et al.   Journal of Chemical Information and Modeling

Chemical and Computational Methods for the Characterization of Covalent Reactive Groups for the Prospective Design of Irreversible Inhibitors

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Drug discovery considerations in the development of covalent inhibitors

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The discovery and development of boceprevir

(2013) David P Rotella   Expert Opinion on Drug Discovery

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

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

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Middle East Respiratory Syndrome Coronavirus Infection Mediated by the Transmembrane Serine Protease TMPRSS2

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Molecular Dynamics Investigation on a Series of HIV Protease Inhibitors: Assessing the Performance of MM-PBSA and MM-GBSA Approaches

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Molecular dynamics simulations and drug discovery

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

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Discovery and development of telaprevir: an NS3-4A protease inhibitor for treating genotype 1 chronic hepatitis C virus

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The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling

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Open Babel: An open chemical toolbox

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Biflavonoids from Torreya nucifera displaying SARS-CoV 3CLpro inhibition

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

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Ligand docking and binding site analysis with PyMOL and Autodock/Vina

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An MM/3D-RISM Approach for Ligand Binding Affinities

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