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Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Molecular Insights into Small‐Molecule Drug Discovery for SARS‐CoV‐2
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Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019‐nCoV
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Scalable molecular dynamics with NAMD
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
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Using the Semiempirical Quantum Mechanics in Improving the Molecular Docking: A Case Study with CDK2
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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
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Repurposing of FDA ‐approved drugs against active site and potential allosteric drug‐binding sites of COVID ‐19 main protease
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Algorithms for hierarchical clustering: an overview, II
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Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton
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Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters
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Improving database enrichment through ensemble docking
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1001 Ways to run AutoDock Vina for virtual screening
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Liberation of SARS-CoV main protease from the viral polyprotein: N-terminal autocleavage does not depend on the mature dimerization mode
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The application of principal component analysis to drug discovery and biomedical data
inferredcites →https://doi.org/10.1016/j.drudis.2020.10.018openalex-snapshot
Union is strength: antiviral and anti-inflammatory drugs for COVID-19
inferredcites →https://doi.org/10.1016/j.drudis.2020.12.005openalex-snapshot
Potential SARS-CoV-2 main protease inhibitors
inferredcites →https://doi.org/10.1016/j.ejmech.2021.113390openalex-snapshot
Structure-based drug design of an inhibitor of the SARS-CoV-2 (COVID-19) main protease using free software: A tutorial for students and scientists
inferredcites →https://doi.org/10.1016/j.jmb.2004.01.003openalex-snapshot
Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases
inferredcites →https://doi.org/10.1016/j.jmb.2021.167118openalex-snapshot
A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process
inferredcites →https://doi.org/10.1016/j.jmgm.2019.01.009openalex-snapshot
Efficient construction of a diverse conformational library for amyloid-β as an intrinsically disordered protein
inferredcites →https://doi.org/10.1016/j.str.2020.10.007openalex-snapshot
Malleability of the SARS-CoV-2 3CL Mpro Active-Site Cavity Facilitates Binding of Clinical Antivirals
inferredcites →https://doi.org/10.1021/acs.biochem.0c00462openalex-snapshot
Sequence Characterization and Molecular Modeling of Clinically Relevant Variants of the SARS-CoV-2 Main Protease
inferredcites →https://doi.org/10.1021/acs.biochem.0c00782openalex-snapshot
Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2
inferredcites →https://doi.org/10.1021/acs.jcim.0c00179openalex-snapshot
Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study
inferredcites →https://doi.org/10.1021/acs.jcim.0c00283openalex-snapshot
Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)
inferredcites →https://doi.org/10.1021/acs.jcim.0c00326openalex-snapshot
Discovery of New Hydroxyethylamine Analogs against 3CLpro Protein Target of SARS-CoV-2: Molecular Docking, Molecular Dynamics Simulation, and Structure–Activity Relationship Studies
inferredcites →https://doi.org/10.1021/acs.jcim.0c00546openalex-snapshot
Structure-Based Virtual Screening to Discover Potential Lead Molecules for the SARS-CoV‑2 Main Protease
inferredcites →https://doi.org/10.1021/acs.jcim.0c00575openalex-snapshot
SARS-CoV‑2 Main Protease: A Molecular Dynamics Study
inferredcites →https://doi.org/10.1021/acs.jcim.0c01010openalex-snapshot
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
inferredcites →https://doi.org/10.1021/acs.jcim.0c01030openalex-snapshot
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV‑2 Main Protease
inferredcites →https://doi.org/10.1021/acs.jcim.0c01457openalex-snapshot
Targeting SARS-CoV-2 M3CLpro by HCV NS3/4a Inhibitors: In Silico Modeling and In Vitro Screening
inferredcites →https://doi.org/10.1021/acs.jcim.1c00159openalex-snapshot
Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro
inferredcites →https://doi.org/10.1021/acs.jcim.1c00263openalex-snapshot
Benchmarking the Ability of Common Docking Programs to Correctly Reproduce and Score Binding Modes in SARS-CoV-2 Protease Mpro
inferredcites →https://doi.org/10.1021/acs.jcim.1c00449openalex-snapshot
Dynamic Profiling of β-Coronavirus 3CL M pro Protease Ligand-Binding Sites
inferredcites →https://doi.org/10.1021/acs.jcim.5b00603openalex-snapshot
An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design
inferredcites →https://doi.org/10.1021/acs.jmedchem.1c00058openalex-snapshot
Direct Observation of Protonation State Modulation in SARS-CoV-2 Main Protease upon Inhibitor Binding with Neutron Crystallography
inferredcites →https://doi.org/10.1021/acs.jpcb.1c03043openalex-snapshot
Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method
inferredcites →https://doi.org/10.1021/acs.jpclett.0c00994openalex-snapshot
In Silico Exploration of the Molecular Mechanism of Clinically Oriented Drugs for Possibly Inhibiting SARS-CoV-2’s Main Protease
inferredcites →https://doi.org/10.1021/acs.jpclett.0c01579openalex-snapshot
Repositioning of 8565 Existing Drugs for COVID-19
inferredcites →https://doi.org/10.1021/acs.jpclett.0c01894openalex-snapshot
Repurposing Low-Molecular-Weight Drugs against the Main Protease of Severe Acute Respiratory Syndrome Coronavirus 2
inferredcites →https://doi.org/10.1021/acs.jpclett.1c00425openalex-snapshot
Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design
inferredcites →https://doi.org/10.1021/acs.jproteome.0c00383openalex-snapshot
In Silico Drug Repurposing for SARS-CoV‑2 Main Proteinase and Spike Proteins
inferredcites →https://doi.org/10.1021/acs.jproteome.0c00683openalex-snapshot
Theoretical Insights into the Anti-SARS-CoV‑2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors
inferredcites →https://doi.org/10.1021/acs.jproteome.0c00779openalex-snapshot
Molecular Basis of SARS-CoV‑2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches
inferredcites →https://doi.org/10.1021/acscentsci.0c00272openalex-snapshot
Research and Development on Therapeutic Agents and Vaccines for COVID-19 and Related Human Coronavirus Diseases
inferredcites →https://doi.org/10.1021/acscombsci.0c00058openalex-snapshot
Targeting the Dimerization of the Main Protease of Coronaviruses: A Potential Broad-Spectrum Therapeutic Strategy
inferredcites →https://doi.org/10.1021/acsmedchemlett.0c00254openalex-snapshot
Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment
inferredcites →https://doi.org/10.1021/acsmedchemlett.0c00521openalex-snapshot
Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2
inferredcites →https://doi.org/10.1021/cen-09812-scicon1openalex-snapshot
Targeting a coronavirus protease
inferredcites →https://doi.org/10.1021/ci400534hopenalex-snapshot
Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design
inferredcites →https://doi.org/10.1021/ci900407copenalex-snapshot
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jm048972vopenalex-snapshot
Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures
inferredcites →https://doi.org/10.1021/jp401742yopenalex-snapshot
New Insights into the Folding of a β-Sheet Miniprotein in a Reduced Space of Collective Hydrogen Bond Variables: Application to a Hydrodynamic Analysis of the Folding Flow
inferredcites →https://doi.org/10.1038/nprot.2016.051openalex-snapshot
Computational protein–ligand docking and virtual drug screening with the AutoDock suite
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1038/s41392-020-0178-yopenalex-snapshot
Designing of improved drugs for COVID-19: Crystal structure of SARS-CoV-2 main protease Mpro
inferredcites →https://doi.org/10.1038/s41422-020-0356-zopenalex-snapshot
Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease
inferredcites →https://doi.org/10.1038/s41467-020-16954-7openalex-snapshot
Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography
inferredcites →https://doi.org/10.1038/s41467-020-18709-wopenalex-snapshot
Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease
inferredcites →https://doi.org/10.1038/s41586-020-2117-zopenalex-snapshot
An open-source drug discovery platform enables ultra-large virtual screens
inferredcites →https://doi.org/10.1038/s41586-020-2223-yopenalex-snapshot
Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors
inferredcites →https://doi.org/10.1038/s41594-020-00544-8openalex-snapshot
Structural biology in the fight against COVID-19
inferredcites →https://doi.org/10.1039/d0cp05714bopenalex-snapshot
A crystallography-based investigation of weak interactions for drug design against COVID-19
inferredcites →https://doi.org/10.1039/d0cs01065kopenalex-snapshot
A critical overview of computational approaches employed for COVID-19 drug discovery
inferredcites →https://doi.org/10.1039/d0ra07352kopenalex-snapshot
Assessing potential inhibitors of SARS-CoV-2 main protease from available drugs using free energy perturbation simulations
inferredcites →https://doi.org/10.1039/d0sc02823aopenalex-snapshot
Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 M pro by QM/MM computational methods
inferredcites →https://doi.org/10.1039/d0sc04641hopenalex-snapshot
Unveiling the molecular mechanism of SARS-CoV-2 main protease inhibition from 137 crystal structures using algebraic topology and deep learning
inferredcites →https://doi.org/10.1039/d0sc04942eopenalex-snapshot
Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease
inferredcites →https://doi.org/10.1039/d0sc04978fopenalex-snapshot
A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design
inferredcites →https://doi.org/10.1039/d0sc06195fopenalex-snapshot
Mechanism of inhibition of SARS-CoV-2 M pro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity
inferredcites →https://doi.org/10.1039/d1sc00145kopenalex-snapshot
High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling
inferredcites →https://doi.org/10.1073/pnas.2010470117openalex-snapshot
Identify potent SARS-CoV-2 main protease inhibitors via accelerated free energy perturbation-based virtual screening of existing drugs
inferredcites →https://doi.org/10.1073/pnas.2012201118openalex-snapshot
Bepridil is potent against SARS-CoV-2 in vitro
inferredcites →https://doi.org/10.1073/pnas.2021579118openalex-snapshot
Identification of existing pharmaceuticals and herbal medicines as inhibitors of SARS-CoV-2 infection
inferredcites →https://doi.org/10.1073/pnas.2025581118openalex-snapshot
Network medicine framework for identifying drug-repurposing opportunities for COVID-19
inferredcites →https://doi.org/10.1093/bib/bbaa260openalex-snapshot
MCCS: a novel recognition pattern-based method for fast track discovery of anti-SARS-CoV-2 drugs
inferredcites →https://doi.org/10.1093/bioinformatics/btu789openalex-snapshot
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
inferredcites →https://doi.org/10.1126/sciadv.abb8097openalex-snapshot
Structure-based drug designing and immunoinformatics approach for SARS-CoV-2
inferredcites →https://doi.org/10.1126/sciadv.abe0751openalex-snapshot
Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L
inferredcites →https://doi.org/10.1126/science.abb3405openalex-snapshot
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors
inferredcites →https://doi.org/10.1126/science.abb4489openalex-snapshot
Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease
inferredcites →https://doi.org/10.1126/scitranslmed.abc5332openalex-snapshot
3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice
inferredcites →https://doi.org/10.1145/1852102.1852106openalex-snapshot
A similarity measure for indefinite rankings
inferredcites →https://doi.org/10.3390/ijms21093099openalex-snapshot
Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design
inferredcites →https://doi.org/10.3390/molecules25173920openalex-snapshot
Design and Evaluation of Anti-SARS-Coronavirus Agents Based on Molecular Interactions with the Viral Protease
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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SAnDReS 2.0: Development of machine‐learning models to explore the scoring function space
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Are protein–ligand docking programs good enough to predict experimental poses of noncovalent ligands bound to the SARS-CoV-2 main protease?
inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108443openalex-snapshot
Unveiling mutation effects on the structural dynamics of the main protease from SARS-CoV-2 with hybrid simulation methods
inferred← citeshttps://doi.org/10.1016/j.jtha.2025.01.021openalex-snapshot
Galloylated polyphenols represent a new class of antithrombotic agents with broad activity against thiol isomerases
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The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops Is Determined by Ligand Binding and Interprotomer Allostery
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01552openalex-snapshot
Compromise in Docking Power of Liganded Crystal Structures of Mpro SARS-CoV-2 Surpasses 90% Success Rate
inferred← citeshttps://doi.org/10.1038/s41598-024-65228-5openalex-snapshot
Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme
inferred← citeshttps://doi.org/10.1080/07391102.2023.2299742openalex-snapshot
Improving protein-ligand docking results using the Semiempirical quantum mechanics: testing on the PDBbind 2016 core set
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The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops is Determined by Ligand Binding and Interprotomer Allostery
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Selective Targeting of SARS-CoV-2 Mpro with Novel Ebsulfur-Based Compounds: A Computational Drug Discovery Approach Combining Molecular Dynamics and DFT Simulations
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In silico study of alkaloids with quercetin nucleus for inhibition of SARS-CoV-2 protease and receptor cell protease
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Computational Repurposing of Potential Dimerization Inhibitors against SARS-CoV-2 Main Protease
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