On the public citation graph
Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 M pro by QM/MM computational methods
0 signed · 220 inferred · view as graph
Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.
Is this your work? Sign in with ORCID and put your name on the
claims that are yours.
Reference health. See whether every reference in this work resolves to a
known work and none has been retracted — and get a dated CiteStamped
badge you can embed.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/chem.201904513openalex-snapshot
Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Proteases Inhibition by Dipeptidyl Nitroalkenes
inferredcites →https://doi.org/10.1002/cmdc.201500204openalex-snapshot
Dipeptidyl Enoates As Potent Rhodesain Inhibitors That Display a Dual Mode of Action
inferredcites →https://doi.org/10.1002/jcc.10349openalex-snapshot
A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations
inferredcites →https://doi.org/10.1002/jcc.26064openalex-snapshot
Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols
inferredcites →https://doi.org/10.1002/jcc.540130812openalex-snapshot
THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
inferredcites →https://doi.org/10.1002/pro.5560060801openalex-snapshot
Structural determinants of specificity in the cysteine protease cruzain
inferredcites →https://doi.org/10.1007/s00214-007-0310-xopenalex-snapshot
The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
inferredcites →https://doi.org/10.1016/0021-9991(77)90121-8openalex-snapshot
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
inferredcites →https://doi.org/10.1016/j.virol.2009.03.034openalex-snapshot
Two adjacent mutations on the dimer interface of SARS coronavirus 3C-like protease cause different conformational changes in crystal structure
inferredcites →https://doi.org/10.1016/s1093-3263(00)00035-8openalex-snapshot
A combined QM/MM study of the nucleophilic addition reaction of methanethiolate and N-methylacetamide
inferredcites →https://doi.org/10.1021/acs.biochem.7b01250openalex-snapshot
Catalytic Mechanism of Cruzain from Trypanosoma cruzi As Determined from Solvent Kinetic Isotope Effects of Steady-State and Pre-Steady-State Kinetics
inferredcites →https://doi.org/10.1021/acs.jcim.9b00404openalex-snapshot
Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors
inferredcites →https://doi.org/10.1021/acs.jcim.9b01138openalex-snapshot
Assessment of the Cruzain Cysteine Protease Reversible and Irreversible Covalent Inhibition Mechanism
inferredcites →https://doi.org/10.1021/acscatal.6b03096openalex-snapshot
Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease
inferredcites →https://doi.org/10.1021/bi00662a014openalex-snapshot
Binding of chloromethyl ketone substrate analogs to crystalline papain
inferredcites →https://doi.org/10.1021/bi400629ropenalex-snapshot
Reaction Pathway and Free Energy Profile for Papain-Catalyzed Hydrolysis ofN-Acetyl-Phe-Gly 4-Nitroanilide
inferredcites →https://doi.org/10.1021/bi501551gopenalex-snapshot
First Quantum Mechanics/Molecular Mechanics Studies of the Inhibition Mechanism of Cruzain by Peptidyl Halomethyl Ketones
inferredcites →https://doi.org/10.1021/ja00047a004openalex-snapshot
Attack of zwitterionic ammonium thiolates on a distorted anilide as a model for the acylation of papain by amides. A simple demonstration of a bell-shaped pH/rate profile
inferredcites →https://doi.org/10.1021/ja00299a024openalex-snapshot
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model
inferredcites →https://doi.org/10.1021/ja074222+openalex-snapshot
Molecular Dynamics Simulations of the Catalytic Pathway of a Cysteine Protease: A Combined QM/MM Study of Human Cathepsin K
inferredcites →https://doi.org/10.1021/jm400294wopenalex-snapshot
Vinyl Sulfone-Based Peptidomimetics as Anti-Trypanosomal Agents: Design, Synthesis, Biological and Computational Evaluation
inferredcites →https://doi.org/10.1021/jp010279lopenalex-snapshot
Ab Initio Evaluation of the Free Energy Surfaces for the General Base/Acid Catalyzed Thiolysis of Formamide and the Hydrolysis of Methyl Thiolformate: A Reference Solution Reaction for Studies of Cysteine Proteases
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/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1073/pnas.1835675100openalex-snapshot
The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor
inferredcites →https://doi.org/10.1093/emboj/cdf327openalex-snapshot
Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra α‐helical domain
inferredcites →https://doi.org/10.1101/2020.03.07.981928openalex-snapshot
Substrate specificity profiling of SARS-CoV-2 main protease enables design of activity-based probes for patient-sample imaging
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
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.2139/ssrn.4846210openalex-extracted
Structure-Guided Design and Photochemical Synthesis of Novel Carbamo(Dithioperoxo)Thioates with Improved Potencies to Sars-Cov-2 3clpro
inferred← citeshttps://doi.org/10.1002/9783527840748.ch6openalex-snapshot
QM / MM for Structure‐Based Drug Design: Techniques and Applications
inferred← citeshttps://doi.org/10.1002/advs.202501625openalex-snapshot
Dynamic Cap‐Mediated Substrate Access and Potent Inhibitor Design of Monkeypox Virus I7L Protease
inferred← citeshttps://doi.org/10.1002/ange.202110027openalex-snapshot
Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs**
inferred← citeshttps://doi.org/10.1002/anie.202110027openalex-snapshot
Inhibition Mechanism of SARS‐CoV‐2 Main Protease with Ketone‐Based Inhibitors Unveiled by Multiscale Simulations: Insights for Improved Designs**
inferred← citeshttps://doi.org/10.1002/chem.202100892openalex-snapshot
Elucidating the Dual Mode of Action of Dipeptidyl Enoates in the Inhibition of Rhodesain Cysteine Proteases
inferred← citeshttps://doi.org/10.1002/cmdc.202100109openalex-snapshot
Computing Metal‐Binding Proteins for Therapeutic Benefit
inferred← citeshttps://doi.org/10.1002/med.21776openalex-snapshot
Therapeutic targets and potential agents for the treatment of COVID‐19
inferred← citeshttps://doi.org/10.1002/pro.70283openalex-snapshot
Evaluating the protonation state of the catalytic Cys25 in cruzain cysteine protease: A target for Chagas disease
inferred← citeshttps://doi.org/10.1002/pro.70680openalex-snapshot
The pivotal role of β‐lactone stereochemistry in the development of SARS ‐ CoV ‐2 M pro inhibitors
inferred← citeshttps://doi.org/10.1002/pro.70788openalex-snapshot
Discovery of D‐peptides that allosterically enhance SARS ‐ CoV ‐2 3CLpro activity by stabilizing its monomeric state
inferred← citeshttps://doi.org/10.1002/prot.26164openalex-snapshot
Repurposing of FDA ‐approved drugs against active site and potential allosteric drug‐binding sites of COVID ‐19 main protease
inferred← citeshttps://doi.org/10.1002/prot.26318openalex-snapshot
Structural insights into the substrate‐binding site of main protease for the structure‐based COVID‐19 drug discovery
inferred← citeshttps://doi.org/10.1002/prot.26385openalex-snapshot
Molecular interactions and inhibition of the SARS‐CoV‐2 main protease by a thiadiazolidinone derivative
inferred← citeshttps://doi.org/10.1002/prot.26665openalex-snapshot
Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory
inferred← citeshttps://doi.org/10.1002/slct.202103658openalex-snapshot
Synthetic Coumarin Derivatives as SARS‐CoV‐2 Major Protease Inhibitors: Design, Synthesis, Bioevaluation and Molecular Docking
inferred← citeshttps://doi.org/10.1002/slct.202203319openalex-snapshot
QM/MM Studies on Enzyme Catalysis and Insight into Designing of New Inhibitors by ONIOM Approach: Recent Update
inferred← citeshttps://doi.org/10.1007/7355_2026_193openalex-snapshot
Focus on SARS-CoV-2 Proteases: Structure, Function, and Inhibitor Development
inferred← citeshttps://doi.org/10.1007/s00894-021-04732-1openalex-snapshot
Multi-conformation representation of Mpro identifies promising candidates for drug repurposing against COVID-19
inferred← citeshttps://doi.org/10.1007/s00894-022-05334-1openalex-snapshot
In silico evaluation of Philippine Natural Products against SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.1007/s11030-021-10259-7openalex-snapshot
New insights into the catalytic mechanism of the SARS-CoV-2 main protease: an ONIOM QM/MM approach
inferred← citeshttps://doi.org/10.1007/s11172-021-3319-8openalex-snapshot
Supercomputer simulation of the covalent inhibition of the main protease of SARS-CoV-2
inferred← citeshttps://doi.org/10.1007/s12010-024-05110-2openalex-snapshot
Decoding Drug Discovery: Exploring A-to-Z In Silico Methods for Beginners
inferred← citeshttps://doi.org/10.1007/s13205-023-03635-7openalex-snapshot
In silico screening, ADMET analysis and MD simulations of phytochemicals of Onosma bracteata Wall. as SARS CoV-2 inhibitors
inferred← citeshttps://doi.org/10.1007/s42452-025-07595-wopenalex-snapshot
An in silico study on phytochemicals from Hibiscus rosa-sinensis as potential inhibitors of SARS-CoV-2 3CLpro
inferred← citeshttps://doi.org/10.1016/b978-0-12-821978-2.00005-2openalex-snapshot
Chemical Bonding in Homogenous Catalysis – Seen Through the Eyes of Vibrational Spectroscopy
inferred← citeshttps://doi.org/10.1016/b978-0-12-821978-2.00101-xopenalex-snapshot
Molecular Dynamics and QM/MM to Understand Genome Organization and Reproduction in Emerging RNA Viruses
inferred← citeshttps://doi.org/10.1016/b978-0-323-90593-0.00004-6openalex-snapshot
Application of density functional theory (DFT) and response surface methodology (RSM) in drug discovery
inferred← citeshttps://doi.org/10.1016/b978-0-443-18977-7.00007-xopenalex-snapshot
In silico biochemistry through a DFT and QM/MM-based computational microscope
inferred← citeshttps://doi.org/10.1016/b978-0-443-29808-0.00076-5openalex-snapshot
Enzymes and reactivity: Leveraging molecular dynamics to inform and refine drug development strategies
inferred← citeshttps://doi.org/10.1016/b978-0-443-29808-0.00081-9openalex-snapshot
Enzymes and reactivity: Leveraging molecular dynamics to inform and refine drug development strategies
inferred← citeshttps://doi.org/10.1016/b978-0-443-36518-8.00023-0openalex-snapshot
Targeting 3CLpro for broad-spectrum antiviral therapy: Structural insights, inhibitor development, and the future of PROTACs
inferred← citeshttps://doi.org/10.1016/j.bmc.2024.117940openalex-snapshot
Structure-guided design and photochemical synthesis of new carbamo(dithioperoxo)thioates with improved potencies to SARS-CoV-2 3CLpro
inferred← citeshttps://doi.org/10.1016/j.bmc.2025.118095openalex-snapshot
Rational design and synthesis of pyrazole derivatives as potential SARS-CoV-2 Mpro inhibitors: An integrated approach merging combinatorial chemistry, molecular docking, and deep learning
inferred← citeshttps://doi.org/10.1016/j.bpc.2020.106510openalex-snapshot
An insight into the interaction between α-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study
inferred← citeshttps://doi.org/10.1016/j.cej.2024.154183openalex-snapshot
Deconstructing PET: Advances in enzyme engineering for sustainable plastic degradation
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2021.104525openalex-snapshot
Unravelling the therapeutic potential of marine drugs as SARS-CoV-2 inhibitors: An insight from essential dynamics and free energy landscape
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2022.106049openalex-snapshot
Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2024.108953openalex-snapshot
On the dual role of (+)-catechin as primary antioxidant and inhibitor of viral proteases
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2025.109779openalex-snapshot
Revealing the impact of active site residues in modeling the inhibition mechanism of SARS-Cov-2 main protease by GC373
inferred← citeshttps://doi.org/10.1016/j.compbiomed.2025.111046openalex-snapshot
Nanoparticles and bioactive materials against COVID-19 and its variants: Hints from a computational-materials design perspective
inferred← citeshttps://doi.org/10.1016/j.comptc.2024.114979openalex-snapshot
Exploring the covalent inhibition mechanisms of inhibitors with two different warheads acting on SARS-CoV-2 Mpro by QM/MM simulations
inferred← citeshttps://doi.org/10.1016/j.cplett.2022.139489openalex-snapshot
Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.03.009openalex-snapshot
Inhibition of the main protease of SARS-CoV-2 (M pro ) by repurposing/designing drug-like substances and utilizing nature’s toolbox of bioactive compounds
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.06.023openalex-snapshot
Maturation of the SARS-CoV-2 virus is regulated by dimerization of its main protease
inferred← citeshttps://doi.org/10.1016/j.drudis.2021.12.017openalex-snapshot
Applications of density functional theory in COVID-19 drug modeling
inferred← citeshttps://doi.org/10.1016/j.ejmech.2023.115979openalex-snapshot
Development of de-novo coronavirus 3-chymotrypsin-like protease (3CLpro) inhibitors since COVID-19 outbreak: A strategy to tackle challenges of persistent virus infection
inferred← citeshttps://doi.org/10.1016/j.heliyon.2020.e05681openalex-snapshot
Investigation on penetration of saffron components through lipid bilayer bound to spike protein of SARS-CoV-2 using steered molecular dynamics simulation
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2022.09.086openalex-snapshot
Exploring the anti-SARS-CoV-2 main protease potential of FDA approved marine drugs using integrated machine learning templates as predictive tools
inferred← citeshttps://doi.org/10.1016/j.jbc.2022.102790openalex-snapshot
pH profiles of 3-chymotrypsin-like protease (3CLpro) from SARS-CoV-2 elucidate its catalytic mechanism and a histidine residue critical for activity
inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.107871openalex-snapshot
Ensemble-based screening of natural products and FDA-approved drugs identified potent inhibitors of SARS-CoV-2 that work with two distinct mechanisms
inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.108050openalex-snapshot
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
inferred← citeshttps://doi.org/10.1016/j.jmgm.2025.109100openalex-snapshot
Combinatorial chemistry-driven In silico design and computational evaluation of covalent peptidomimetic SARS-CoV-2 main protease inhibitors via structure-based virtual screening and multivariate analysis
inferred← citeshttps://doi.org/10.1016/j.molliq.2025.128007openalex-snapshot
Inhibitory potential of gallic acid against SARS-CoV-2 main protease: A structure-function insight using combined spectroscopic and computational approach
inferred← citeshttps://doi.org/10.1016/j.molstruc.2022.134507openalex-snapshot
Novel ciprofloxacin and norfloxacin-tetrazole hybrids as potential antibacterial and antiviral agents: Targeting S. aureus topoisomerase and SARS-CoV-2-MPro
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2022.155580openalex-snapshot
In silico evidence of antiviral activity against SARS-CoV-2 main protease of oligosaccharides from Porphyridium sp.
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1021/acs.chemrev.1c00965openalex-snapshot
Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01010openalex-snapshot
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
inferred← citeshttps://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
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00355openalex-snapshot
Structure-Based Discovery of Novel Nonpeptide Inhibitors Targeting SARS-CoV-2 Mpro
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00449openalex-snapshot
Dynamic Profiling of β-Coronavirus 3CL M pro Protease Ligand-Binding Sites
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00515openalex-snapshot
Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00666openalex-snapshot
Unrevealing the Proteolytic Activity of RgpB Gingipain from Computational Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00140openalex-snapshot
Mechanistic Modeling of Monoglyceride Lipase Covalent Modification Elucidates the Role of Leaving Group Expulsion and Discriminates Inhibitors with High and Low Potency
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00201openalex-snapshot
Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00802openalex-snapshot
Modeling the Enzymatic Mechanism of the SARS-CoV-2 RNA-Dependent RNA Polymerase by DFT/MM-MD: An Unusual Active Site Leading to High Replication Rates
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01198openalex-snapshot
Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer’s Disease
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00105openalex-snapshot
Elucidating Atomistic Insight into the Dynamical Responses of the SARS-CoV-2 Main Protease for the Binding of Remdesivir Analogues: Leveraging Molecular Mechanics To Decode the Inhibition Mechanism
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00168openalex-snapshot
Diphenyl Diselenide and SARS-CoV-2: in silico Exploration of the Mechanisms of Inhibition of Main Protease (Mpro) and Papain-like Protease (PLpro)
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01269openalex-snapshot
Discovery of Nirmatrelvir Resistance Mutations in SARS-CoV-2 3CLpro: A Computational-Experimental Approach
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01594openalex-snapshot
Potency Prediction of Covalent Inhibitors against SARS-CoV-2 3CL-like Protease and Multiple Mutants by Multiscale Simulations
inferred← citeshttps://doi.org/10.1021/acs.jctc.2c00286openalex-snapshot
How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c01005openalex-snapshot
Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure–Activity Relationship Insights and Evolution Perspectives
inferred← citeshttps://doi.org/10.1021/acs.jnatprod.2c00521openalex-snapshot
The Natural Products Withaferin A and Withanone from the Medicinal HerbWithania somniferaAre Covalent Inhibitors of the SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.1021/acs.jpclett.1c00425openalex-snapshot
Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design
inferred← citeshttps://doi.org/10.1021/acs.jpclett.2c01193openalex-snapshot
Primer for Designing Main Protease (Mpro) Inhibitors of SARS-CoV-2
inferred← citeshttps://doi.org/10.1021/acs.jpclett.4c03654openalex-snapshot
A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats
inferred← citeshttps://doi.org/10.1021/acs.jpclett.5c02743openalex-snapshot
Native Folding Stability of the Main Protease of Coronavirus SARS-CoV-2 on a Gold Surface
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1021/acscatal.0c03420openalex-snapshot
Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale Methods
inferred← citeshttps://doi.org/10.1021/acscatal.0c05522openalex-snapshot
Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Changes in the Reaction Mechanism
inferred← citeshttps://doi.org/10.1021/acscatal.1c02150openalex-snapshot
Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes
inferred← citeshttps://doi.org/10.1021/acscatal.1c04661openalex-snapshot
Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 M pro Explored by QM/MM Simulations
inferred← citeshttps://doi.org/10.1021/acscatal.3c02748openalex-snapshot
Impact of the Warhead of Dipeptidyl Keto Michael Acceptors on the Inhibition Mechanism of Cysteine Protease Cathepsin L
inferred← citeshttps://doi.org/10.1021/acscatal.4c01159openalex-snapshot
Structural Basis for the Acylation Reaction of Alphacoronavirus 3C-like Protease
inferred← citeshttps://doi.org/10.1021/acscatal.4c04695openalex-snapshot
Catalytic Mechanism of SARS-CoV-2 3-Chymotrypsin-Like Protease as Determined by Steady-State and Pre-Steady-State Kinetics
inferred← citeshttps://doi.org/10.1021/acscatal.4c06020openalex-snapshot
Mechanistic Insights into Nitrile and Alkyne Covalent Inhibitors of the SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.1021/acscatal.5c09296openalex-snapshot
Stereochemistry-Guided Switch from Irreversible to Slow-Binding Cathepsin L Inhibition
inferred← citeshttps://doi.org/10.1021/acschembio.6c00577openalex-snapshot
From Inhibitor to Reporter: Nirmatrelvir-Derived Fluorogenic Substrates for the SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.1021/acsomega.0c04808openalex-snapshot
Structure-Based Virtual Screening and Biochemical Validation to Discover a Potential Inhibitor of the SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.1021/acsomega.3c00944openalex-snapshot
Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective
inferred← citeshttps://doi.org/10.1021/acsomega.3c09084openalex-snapshot
Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development
inferred← citeshttps://doi.org/10.1021/acsomega.4c03023openalex-snapshot
Progress in Research on Inhibitors Targeting SARS-CoV-2 Main Protease (M pro )
inferred← citeshttps://doi.org/10.1021/acssynbio.5c00423openalex-snapshot
Engineering the Tobacco Etch Virus Protease toward a Platform for Traceless Cleavage Using Distal Site Prediction and Smart Library Design
inferred← citeshttps://doi.org/10.1021/jacs.1c05301openalex-snapshot
Water-Triggered, Irreversible Conformational Change of SARS-CoV-2 Main Protease on Passing from the Solid State to Aqueous Solution
inferred← citeshttps://doi.org/10.1021/jacs.3c02229openalex-snapshot
Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms
inferred← citeshttps://doi.org/10.1021/jacs.5c21421openalex-snapshot
From Brewing to Plastic Degradation: Uncovering the Polyurethanase Potential of R. chinensis Lipase through Atomistic Simulations
inferred← citeshttps://doi.org/10.1021/jacsau.3c00185openalex-snapshot
Dynamical Nonequilibrium Molecular Dynamics Simulations Identify Allosteric Sites and Positions Associated with Drug Resistance in the SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.1038/s41467-020-19662-4openalex-snapshot
Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site
inferred← citeshttps://doi.org/10.1038/s41598-022-23570-6openalex-snapshot
Mechanistic investigation of SARS-CoV-2 main protease to accelerate design of covalent inhibitors
inferred← citeshttps://doi.org/10.1038/s41598-023-44476-xopenalex-snapshot
Antcin-B, a phytosterol-like compound from Taiwanofungus camphoratus inhibits SARS-CoV-2 3-chymotrypsin-like protease (3CLPro) activity in silico and in vitro
inferred← citeshttps://doi.org/10.1038/s41598-024-81990-yopenalex-snapshot
An isothermal calorimetry assay for determining steady state kinetic and Ensitrelvir inhibition parameters for SARS-CoV-2 3CL-protease
inferred← citeshttps://doi.org/10.1038/s42004-024-01104-7openalex-snapshot
Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2
inferred← citeshttps://doi.org/10.1039/d0cp04326eopenalex-snapshot
Discovery of potent inhibitors for SARS-CoV-2's main protease by ligand-based/structure-based virtual screening, MD simulations, and binding energy calculations
inferred← citeshttps://doi.org/10.1039/d0ra10141aopenalex-snapshot
Ligand-based design, molecular dynamics and ADMET studies of suggested SARS-CoV-2 M pro inhibitors
inferred← citeshttps://doi.org/10.1039/d0sc04942eopenalex-snapshot
Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1039/d0sc04978fopenalex-snapshot
A microscopic description of SARS-CoV-2 main protease inhibition with Michael acceptors. Strategies for improving inhibitor design
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1039/d0tb02639eopenalex-snapshot
Nanoscience and quantum science-led biocidal and antiviral strategies
inferred← citeshttps://doi.org/10.1039/d1cc01449hopenalex-snapshot
Influence of charge configuration on substrate binding to SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1039/d1cp00266jopenalex-snapshot
Covalent and non-covalent binding free energy calculations for peptidomimetic inhibitors of SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.1039/d1cp02967copenalex-snapshot
Microscopic interactions between ivermectin and key human and viral proteins involved in SARS-CoV-2 infection
inferred← citeshttps://doi.org/10.1039/d1cy02271gopenalex-snapshot
The critical role of Asp206 stabilizing residues on the catalytic mechanism of the Ideonella sakaiensis PETase
inferred← citeshttps://doi.org/10.1039/d1ra08752eopenalex-snapshot
Insights into the binding and covalent inhibition mechanism of PF-07321332 to SARS-CoV-2 M pro
inferred← citeshttps://doi.org/10.1039/d1sc00145kopenalex-snapshot
High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling
inferred← citeshttps://doi.org/10.1039/d1sc02775aopenalex-snapshot
Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design
inferred← citeshttps://doi.org/10.1039/d1sc03628aopenalex-snapshot
Discovery of SARS-CoV-2 M pro peptide inhibitors from modelling substrate and ligand binding
inferred← citeshttps://doi.org/10.1039/d1sc05892dopenalex-snapshot
Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation
inferred← citeshttps://doi.org/10.1039/d2cp03080bopenalex-snapshot
Estimating the binding energetics of reversible covalent inhibitors of the SARS-CoV-2 main protease: an in silico study
inferred← citeshttps://doi.org/10.1039/d2cp04476eopenalex-snapshot
Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches
inferred← citeshttps://doi.org/10.1039/d2sc00108jopenalex-snapshot
Autophagy and evasion of the immune system by SARS-CoV-2. Structural features of the non-structural protein 6 from wild type and Omicron viral strains interacting with a model lipid bilayer
inferred← citeshttps://doi.org/10.1039/d3cc01576aopenalex-snapshot
Reaction mechanism – explored with the unified reaction valley approach
inferred← citeshttps://doi.org/10.1039/d3cp03394eopenalex-snapshot
Computational study on the mechanisms of inhibition of SARS-CoV-2 M pro by aldehyde warheads based on DFT
inferred← citeshttps://doi.org/10.1039/d3sc00166kopenalex-snapshot
Unraveling the catalytic mechanism of SARS-CoV-2 papain-like protease with allosteric modulation of C270 mutation using multiscale computational approaches
inferred← citeshttps://doi.org/10.1039/d4ra08449gopenalex-snapshot
Dihydropyrimidine-2-thione derivatives as SARS-CoV-2 main protease inhibitors: synthesis, SAR and in vitro profiling
inferred← citeshttps://doi.org/10.1042/bcj20200514openalex-snapshot
The role of chemical biology in the fight against SARS-CoV-2
inferred← citeshttps://doi.org/10.1042/bsr20231395openalex-snapshot
3-chymotrypsin-like protease in SARS-CoV-2
inferred← citeshttps://doi.org/10.1063/5.0123698openalex-snapshot
Polarizable MD and QM/MM investigation of acrylamide-based leads to target the main protease of SARS-CoV-2
inferred← citeshttps://doi.org/10.1063/5.0148064openalex-snapshot
Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α -ketoamide inhibitors
inferred← citeshttps://doi.org/10.1063/5.0288283openalex-snapshot
Off the beaten (catalytic) path: Charting the mechanistic space of enzyme reactions
inferred← citeshttps://doi.org/10.1080/07391102.2021.1897043openalex-snapshot
Molecular modeling of potent novel sulfonamide derivatives as non-peptide small molecule anti-COVID 19 agents
inferred← citeshttps://doi.org/10.1080/14756366.2025.2460045openalex-snapshot
Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds
inferred← citeshttps://doi.org/10.1080/17460441.2022.2034783openalex-snapshot
Electrophilic warheads in covalent drug discovery: an overview
inferred← citeshttps://doi.org/10.1080/17512433.2021.1959318openalex-snapshot
Molecular docking and dynamics study to explore phytochemical ligand molecules against the main protease of SARS-CoV-2 from extensive phytochemical datasets
inferred← citeshttps://doi.org/10.1080/19420889.2025.2603140openalex-snapshot
Quantum mechanics in drug design: Progress, challenges, and future frontiers
inferred← citeshttps://doi.org/10.1101/2023.12.01.569046openalex-snapshot
Substrate recognition and selectivity in SARS-CoV-2 main protease: Unveiling the role of subsite interactions through dynamical nonequilibrium molecular dynamics simulations
inferred← citeshttps://doi.org/10.1101/2024.01.31.578159openalex-snapshot
An isothermal calorimetry assay for determining steady state kinetic and enzyme inhibition parameters for SARS-CoV-2 3CL-protease
inferred← citeshttps://doi.org/10.1101/2024.09.10.24313452openalex-snapshot
Network biology and bioinformatics-based framework to identify the impacts of SARS-CoV-2 infections on lung cancer and tuberculosis
inferred← citeshttps://doi.org/10.1109/mcse.2020.3024155openalex-snapshot
Biomolecular Simulations in the Time of COVID-19, and After
inferred← citeshttps://doi.org/10.1126/sciadv.add7197openalex-snapshot
Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system
inferred← citeshttps://doi.org/10.1142/s273741652350014xopenalex-snapshot
SARS-CoV-2 Main Protease Inhibitors: Structure-Based Enhancement to Anti-Viral Pre-Clinical GC376 Encourages Further Development
inferred← citeshttps://doi.org/10.1142/s2737416525500280openalex-snapshot
Selective Targeting of SARS-CoV-2 Mpro with Novel Ebsulfur-Based Compounds: A Computational Drug Discovery Approach Combining Molecular Dynamics and DFT Simulations
inferred← citeshttps://doi.org/10.12794/metadc1944361openalex-snapshot
Computational Modeling of Cancer-Related Mutations in DNA Repair Enzymes Using Molecular Dynamics and Quantum Mechanics/Molecular Mechanics
inferred← citeshttps://doi.org/10.1515/pac-2025-0500openalex-snapshot
The quantum revolution in enzymatic chemistry: combining quantum and classical mechanics to understand biochemical processes
inferred← citeshttps://doi.org/10.1590/1678-4685-gmb-2021-0404openalex-snapshot
Investigation of changes in protein stability and substrate affinity of 3CL-protease of SARS-CoV-2 caused by mutations
inferred← citeshttps://doi.org/10.20944/preprints202308.1518.v1openalex-snapshot
A Molecular Modeling and Molecular Dynamics Simulations Investigation of the Potential Therapeutic Applications of Main Protease Inhibitors for SARS-CoV-2
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2837087/v1openalex-snapshot
Identification of novel phytochemicals from Hibiscus rosa sinensis flower as a prospective inhibitor targeting the 3CLpro enzyme of SARS-CoV-2 using computational approaches.
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2837087/v2openalex-snapshot
Identification of novel phytochemicals from Hibiscus rosa sinensis flower as a prospective inhibitor targeting the 3CLpro enzyme of SARS-CoV-2 using computational approaches.
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2837087/v3openalex-snapshot
Identification of novel phytochemicals from Hibiscus rosa sinensis flower as a prospective inhibitor targeting the 3CLpro enzyme of SARS-CoV-2 using computational approaches.
inferred← citeshttps://doi.org/10.21203/rs.3.rs-4036418/v1openalex-snapshot
Exploring multiple reaction pathways in the proteolysis of SARS-CoV-2 main protease through large-scale quantum molecular dynamics
inferred← citeshttps://doi.org/10.2142/biophysico.bppb-v18.022openalex-snapshot
Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.2142/biophysico.bppb-v18.024openalex-snapshot
Greetings from the President of Biophysical Society of Japan: Traditionally open culture for fostering creative biophysics
inferred← citeshttps://doi.org/10.2147/aabc.s393084openalex-snapshot
In silico Screening of Potential SARS-CoV-2 Main Protease Inhibitors from Thymus schimperi
inferred← citeshttps://doi.org/10.2174/9789815179934123010010openalex-snapshot
Quantum Chemistry in Drug Design: Density Function Theory (DFT) and Other Quantum Mechanics (QM)-related Approaches
inferred← citeshttps://doi.org/10.26434/chemrxiv-2021-zpp2jopenalex-snapshot
Insight into the Binding Energetics of Targeted Reversible Covalent Inhibitors of the SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.26434/chemrxiv-2022-8lr3vopenalex-snapshot
QM/MM Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms
inferred← citeshttps://doi.org/10.26434/chemrxiv.12501734openalex-snapshot
Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale DFT/MM Methods
inferred← citeshttps://doi.org/10.26434/chemrxiv.12501734.v1openalex-snapshot
Unraveling the SARS-CoV-2 Main Protease Mechanism Using Multiscale DFT/MM Methods
inferred← citeshttps://doi.org/10.26434/chemrxiv.12782258openalex-snapshot
Has Ivermectin Virus-Directed Effects against SARS-CoV-2? Rationalizing the Action of a Potential Multitarget Antiviral Agent
inferred← citeshttps://doi.org/10.26434/chemrxiv.12782258.v1openalex-snapshot
Has Ivermectin Virus-Directed Effects against SARS-CoV-2? Rationalizing the Action of a Potential Multitarget Antiviral Agent
inferred← citeshttps://doi.org/10.26434/chemrxiv.12924974openalex-snapshot
Microscopic Factors Modulating the Interactions Between the SARS-CoV-2 Main Protease and α−Ketoamide Inhibitors
inferred← citeshttps://doi.org/10.26434/chemrxiv.12924974.v1openalex-snapshot
Microscopic Factors Modulating the Interactions Between the SARS-Cov-2 Main Protease and α−Ketoamide Inhibitors
inferred← citeshttps://doi.org/10.26434/chemrxiv.13200227openalex-snapshot
Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design
inferred← citeshttps://doi.org/10.26434/chemrxiv.13340939openalex-snapshot
Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations
inferred← citeshttps://doi.org/10.26434/chemrxiv.13340942openalex-snapshot
Multiscale Simulations of SARS-CoV-2 3CL Protease Inhibition with Aldehyde Derivatives. Role of Protein and Inhibitor Conformational Dynamics in the Reaction Mechanism
inferred← citeshttps://doi.org/10.28991/scimedj-2020-02-si-11openalex-snapshot
The Possible Molecular Mechanism of SARS-CoV-2 Main Protease: New Structural Insights from Computational Methods
inferred← citeshttps://doi.org/10.33435/tcandtc.1121985openalex-snapshot
An in silico investigation of allosteric inhibition potential of Dihydroergotamine against Sars-CoV-2 Main Protease (MPro)
inferred← citeshttps://doi.org/10.3389/fcell.2022.807149openalex-snapshot
Protein Posttranslational Signatures Identified in COVID-19 Patient Plasma
inferred← citeshttps://doi.org/10.3389/fchem.2021.622898openalex-snapshot
Structural Basis of Potential Inhibitors Targeting SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.3389/fchem.2021.819165openalex-snapshot
Targeting SARS-CoV-2 Proteases for COVID-19 Antiviral Development
inferred← citeshttps://doi.org/10.3389/fmolb.2020.00194openalex-snapshot
Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations
inferred← citeshttps://doi.org/10.3390/app11146291openalex-snapshot
Mechanistic Insight into SARS-CoV-2 Mpro Inhibition by Organoselenides: The Ebselen Case Study
inferred← citeshttps://doi.org/10.3390/biomedicines10081787openalex-snapshot
The Inhibitory Potential of Ferulic Acid Derivatives against the SARS-CoV-2 Main Protease: Molecular Docking, Molecular Dynamics, and ADMET Evaluation
inferred← citeshttps://doi.org/10.3390/ijms22063232openalex-snapshot
Mechanisms of Proteolytic Enzymes and Their Inhibition in QM/MM Studies
inferred← citeshttps://doi.org/10.3390/ijms22189792openalex-snapshot
The Se–S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study
inferred← citeshttps://doi.org/10.3390/ijms24098011openalex-snapshot
Ferulic Acid: A Review of Pharmacology, Toxicology, and Therapeutic Effects on Pulmonary Diseases
inferred← citeshttps://doi.org/10.3390/ijms26199742openalex-snapshot
Discovery of Galloyl–Flavonoid Conjugates as SARS-CoV-2 3CLpro Inhibitors: Understanding Binding Interactions Through Computational Approaches
inferred← citeshttps://doi.org/10.3390/microorganisms13061271openalex-snapshot
Marine-Derived Peptides from Phaeodactylum tricornutum as Potential SARS-CoV-2 Mpro Inhibitors: An In Silico Approach
inferred← citeshttps://doi.org/10.3390/molecules26185724openalex-snapshot
In Silico Evaluation of Iranian Medicinal Plant Phytoconstituents as Inhibitors against Main Protease and the Receptor-Binding Domain of SARS-CoV-2
inferred← citeshttps://doi.org/10.3390/molecules27238251openalex-snapshot
Insights into the Dynamics and Binding of Two Polyprotein Substrate Cleavage Points in the Context of the SARS-CoV-2 Main and Papain-like Proteases
inferred← citeshttps://doi.org/10.3390/molecules30193896openalex-snapshot
1,2,4-Thiadiazolidin-3,5-Diones as Inhibitors of Cysteine Proteases
inferred← citeshttps://doi.org/10.3390/ph15020129openalex-snapshot
Antiviral Effects of Artemisinin and Its Derivatives against SARS-CoV-2 Main Protease: Computational Evidences and Interactions with ACE2 Allelic Variants
inferred← citeshttps://doi.org/10.3390/polym13213823openalex-snapshot
Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.3390/v16060844openalex-snapshot
3-Chymotrypsin-like Protease (3CLpro) of SARS-CoV-2: Validation as a Molecular Target, Proposal of a Novel Catalytic Mechanism, and Inhibitors in Preclinical and Clinical Trials
inferred← citeshttps://doi.org/10.35772/ghm.2022.01066openalex-snapshot
Drug development targeting SARS-CoV-2 main protease
inferred← citeshttps://doi.org/10.4155/fmc-2020-0380openalex-snapshot
Selection of SARS-CoV-2 Main Protease Inhibitor Using Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.70675/5588b049z7574z4563z8f93zeba117c9b64copenalex-snapshot
Analyse de systèmes complexes par dynamique moléculaire polarisable, vers une conception rationnelle de médicaments : des quadruplexes de Guanine au SARS-CoV-2
inferred← citeshttps://doi.org/10.70675/9e156438z6819z4345zbfacz177d25ca375fopenalex-snapshot
Multiscale approaches to help clarify mechanisms of activation/inhibition for important biological systems
inferred← citeshttps://doi.org/10.70675/d0667c2cz9cd4z4283za82bzd632c430f26bopenalex-snapshot
Advancing Large-Scale Molecular Dynamics through Machine Learning
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.