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

https://doi.org/10.1021/ci500118s
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints
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A hierarchical approach to all‐atom protein loop prediction
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The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling
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Progress in super long loop prediction
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Automated docking of substrates to proteins by simulated annealing
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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Epik: a software program for pK a prediction and protonation state generation for drug-like molecules
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Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution
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Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
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Inhibitors of hepatitis C virus NS3·4A protease. Effect of P4 capping groups on inhibitory potency and pharmacokinetics
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On the Role of the Crystal Environment in Determining Protein Side-chain Conformations
inferredcites →https://doi.org/10.1016/s0960-894x(01)00843-5openalex-snapshot
Evolution, synthesis and SAR of tripeptide α-ketoacid Inhibitors of the hepatitis C virus NS3/NS4A serine protease
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Challenges in Modern Drug Discovery: A Case Study of Boceprevir, an HCV Protease Inhibitor for the Treatment of Hepatitis C Virus Infection
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ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers
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Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm030644sopenalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
inferredcites →https://doi.org/10.1021/jm051256oopenalex-snapshot
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein−Ligand Complexes
inferredcites →https://doi.org/10.1038/nchembio866openalex-snapshot
Structure-guided development of affinity probes for tyrosine kinases using chemical genetics
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The resurgence of covalent drugs
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The Bruton tyrosine kinase inhibitor PCI-32765 blocks B-cell activation and is efficacious in models of autoimmune disease and B-cell malignancy
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Discovery and Development of VX-950, a Novel, Covalent, and Reversible Inhibitor of Hepatitis C Virus NS3.4A Serine Protease

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inferred← citeshttps://doi.org/10.1016/j.ejmech.2017.06.019openalex-snapshot
Covalent inhibitors design and discovery
inferred← citeshttps://doi.org/10.1016/j.ejmech.2017.08.035openalex-snapshot
Discovery of N -(5-((5-chloro-4-((2-(isopropylsulfonyl)phenyl)amino)pyrimidin-2-yl)amino)-4-methoxy-2-(4-methyl-1,4-diazepan-1-yl)phenyl)acrylamide (CHMFL-ALK/EGFR-050) as a potent ALK/EGFR dual kinase inhibitor capable of overcoming a variety of ALK/EGFR associated drug resistant mutants in NSCLC
inferred← citeshttps://doi.org/10.1016/j.ejmech.2020.112836openalex-snapshot
An electrophilic warhead library for mapping the reactivity and accessibility of tractable cysteines in protein kinases
inferred← citeshttps://doi.org/10.1016/j.ejmech.2021.113455openalex-snapshot
Discovery of selective fragment-sized immunoproteasome inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2021.113711openalex-snapshot
The synthesis and bioactivity of pyrrolo[2,3-d]pyrimidine derivatives as tyrosine kinase inhibitors for NSCLC cells with EGFR mutations
inferred← citeshttps://doi.org/10.1016/j.ejmech.2021.113786openalex-snapshot
A sulfonyl fluoride derivative inhibits EGFRL858R/T790M/C797S by covalent modification of the catalytic lysine
inferred← citeshttps://doi.org/10.1016/j.ejmech.2021.114088openalex-snapshot
Efficient targeted oncogenic KRASG12C degradation via first reversible-covalent PROTAC
inferred← citeshttps://doi.org/10.1016/j.ejmech.2022.114130openalex-snapshot
In silico screening-based discovery of novel covalent inhibitors of the SARS-CoV-2 3CL protease
inferred← citeshttps://doi.org/10.1016/j.ejmech.2022.114752openalex-snapshot
Covalent inhibitors of bacterial peptidoglycan biosynthesis enzyme MurA with chloroacetamide warhead
inferred← citeshttps://doi.org/10.1016/j.ejmech.2022.114803openalex-snapshot
Discovery of novel SARS-CoV-2 3CL protease covalent inhibitors using deep learning-based screen
inferred← citeshttps://doi.org/10.1016/j.ejmech.2022.114853openalex-snapshot
Easy access to α-ketoamides as SARS-CoV-2 and MERS Mpro inhibitors via the PADAM oxidation route
inferred← citeshttps://doi.org/10.1016/j.ejmech.2022.114857openalex-snapshot
Rational design of the zonulin inhibitor AT1001 derivatives as potential anti SARS-CoV-2
inferred← citeshttps://doi.org/10.1016/j.ejmech.2022.115048openalex-snapshot
Pseudo-irreversible butyrylcholinesterase inhibitors: Structure–activity relationships, computational and crystallographic study of the N-dialkyl O-arylcarbamate warhead
inferred← citeshttps://doi.org/10.1016/j.ejmech.2023.115129openalex-snapshot
Discovery, synthesis and mechanism study of 2,3,5-substituted [1,2,4]-thiadiazoles as covalent inhibitors targeting 3C-Like protease of SARS-CoV-2
inferred← citeshttps://doi.org/10.1016/j.ejmech.2024.116263openalex-snapshot
Synthesis and biological evaluation of novel peptidomimetic inhibitors of the coronavirus 3C-like protease
inferred← citeshttps://doi.org/10.1016/j.ejmech.2024.117004openalex-snapshot
Discovery of peptidomimetic spiropyrrolidine derivatives as novel 3CLpro inhibitors against SARS-CoV -2
inferred← citeshttps://doi.org/10.1016/j.ejmech.2025.118274openalex-snapshot
Allosteric inhibition of JAK2 with lysine-reactive compounds that bind the pseudokinase domain
inferred← citeshttps://doi.org/10.1016/j.ejmech.2025.118486openalex-snapshot
Targeting neuroinflammation by activation of the sigma-1 receptor (S1R) and inhibition of butyrylcholinesterase (hBChE) leads to highly potent anti-amnesic compounds in an Alzheimer's disease mouse model
inferred← citeshttps://doi.org/10.1016/j.ejmech.2025.118494openalex-snapshot
In vitro kinetic profiling by enzymatic approaches to select FAPIs with a long residence time
inferred← citeshttps://doi.org/10.1016/j.ejmech.2026.118935openalex-snapshot
Design, semi-synthesis and biological evaluation of grandiflorenic acid derivatives as potent covalent NLRP3 inhibitors
inferred← citeshttps://doi.org/10.1016/j.ejmech.2026.118965openalex-snapshot
Identification of the target ANTXR1 and covalent acylation mechanism of 8-esterified cycloberberines against cancer
inferred← citeshttps://doi.org/10.1016/j.ejmech.2026.119098openalex-snapshot
Exploring chemical space based on Transformation to design broad-spectrum 3CLpro inhibitors against coronavirus
inferred← citeshttps://doi.org/10.1016/j.ejphar.2023.176156openalex-snapshot
Bisabosqual A: A novel asparagine synthetase inhibitor suppressing the proliferation and migration of human non-small cell lung cancer A549 cells
inferred← citeshttps://doi.org/10.1016/j.ejphar.2025.177567openalex-snapshot
Biostability, in vivo antiviral activity against respiratory syncytial virus, and pharmacokinetic profiles of (−)-borneol esters
inferred← citeshttps://doi.org/10.1016/j.ejps.2020.105463openalex-snapshot
Computational studies of potent covalent inhibitors on wild type or T790M/L858R mutant epidermal growth factor receptor
inferred← citeshttps://doi.org/10.1016/j.freeradbiomed.2025.12.007openalex-snapshot
Identification and mechanistic exploration of a mono-carbonyl analog A1 of dietary curcumin as a potent Nrf2-dependent neuroprotective agent within a cellular model of Parkinson's disease
inferred← citeshttps://doi.org/10.1016/j.ibmb.2019.01.001openalex-snapshot
The molecular basis for the neofunctionalization of the juvenile hormone esterase duplication in Drosophila
inferred← citeshttps://doi.org/10.1016/j.ijantimicag.2026.107756openalex-snapshot
cirA promoter disruption and SHV-12 production contribute to cefiderocol resistance in carbapenem-resistant Klebsiella pneumoniae
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2023.124443openalex-snapshot
Design of novel pyrimidine based remdesivir analogues with dual target specificity for SARS CoV-2: A computational approach
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2024.138529openalex-snapshot
Exploring bifunctional molecules for anti-SARS-CoV-2 and anti-inflammatory activity through structure-based virtual screening, SAR investigation, and biological evaluation
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.140526openalex-snapshot
High-throughput virtual screening and empirical validation of probable inhibitors of Plasmodium falciparum and vivax glutathione transferase using bromosulfophthalein as the benchmark ligand
inferred← citeshttps://doi.org/10.1016/j.ijfoodmicro.2022.109817openalex-snapshot
Antifungal activity and molecular mechanisms of mulberrin derivatives against Colletotrichum gloeosporioides for mango storage
inferred← citeshttps://doi.org/10.1016/j.jbc.2022.102454openalex-snapshot
High-resolution structures of a siderophore-producing cyclization domain from Yersinia pestis offer a refined proposal of substrate binding
inferred← citeshttps://doi.org/10.1016/j.jbc.2024.107650openalex-snapshot
Anti-mutagenic agent targeting LexA to combat antimicrobial resistance in mycobacteria
inferred← citeshttps://doi.org/10.1016/j.jbc.2026.113322openalex-snapshot
A covalent inhibitor targeting Cys-349 of LIMK1 confers selectivity over LIMK2
inferred← citeshttps://doi.org/10.1016/j.jmb.2026.169807openalex-snapshot
GalaxyCDock: Webserver for Covalent Protein–Ligand Binding Mode Prediction
inferred← citeshttps://doi.org/10.1016/j.jmgm.2020.107776openalex-snapshot
Effects of selective calcium channel blockers on ions’ permeation through the human Cav1.2 ion channel: A computational study
inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.108054openalex-snapshot
Optimization of covalent docking for organophosphates interaction with Anopheles acetylcholinesterase
inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108549openalex-snapshot
Structure-based computational design of novel covalent binders for the treatment of sickle cell disease
inferred← citeshttps://doi.org/10.1016/j.jmgm.2023.108672openalex-snapshot
Discovery of pyrimidoindol and benzylpyrrolyl inhibitors targeting SARS-CoV-2 main protease (Mpro) through pharmacophore modelling, covalent docking, and biological evaluation
inferred← citeshttps://doi.org/10.1016/j.jmgm.2024.108762openalex-snapshot
Covalent docking-driven virtual screening of extensive small-molecule libraries against Bruton tyrosine kinase for the identification of highly selective and potent novel therapeutic candidates
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.jmgm.2025.109264openalex-snapshot
Computational studies of target-specific radiopharmaceuticals for theranostics
inferred← citeshttps://doi.org/10.1016/j.molstruc.2021.132313openalex-snapshot
Design and synthesis of the novel, selective WZ4002 analogue as EGFR-L858R/T790M tyrosine kinase inhibitors for targeted drug therapy in non-small-cell lung cancer (NSCLC)
inferred← citeshttps://doi.org/10.1016/j.molstruc.2023.135762openalex-snapshot
Bioactivity studies and Insilico studies of the isolated compound from ancient plant Vitex negundo against breast cancer
inferred← citeshttps://doi.org/10.1016/j.pedsph.2025.08.003openalex-snapshot
Tetracycline-induced alterations in black soil bacteria community and nitrogen conversion processes
inferred← citeshttps://doi.org/10.1016/j.pep.2020.105697openalex-snapshot
Expression of a heptelidic acid-insensitive recombinant GAPDH from Trichoderma virens, and its biochemical and biophysical characterization
inferred← citeshttps://doi.org/10.1016/j.procbio.2021.08.022openalex-snapshot
In silico analyses of predicted substitutions in fibrinolytic protein ‘Lumbrokinase-6’ suggest enhanced activity
inferred← citeshttps://doi.org/10.1016/j.saa.2019.117807openalex-snapshot
Effects of reverse genetic mutations on the spectral and photochemical behavior of a photoactivatable fluorescent protein PAiRFP1
inferred← citeshttps://doi.org/10.1016/j.saa.2021.119572openalex-snapshot
Impact of amino acid substitutions on the behavior of a photoactivatable near infrared fluorescent protein PAiRFP1
inferred← citeshttps://doi.org/10.1016/j.semcancer.2020.01.010openalex-snapshot
Structure-based drug repositioning: Potential and limits
inferred← citeshttps://doi.org/10.1016/j.steroids.2025.109638openalex-snapshot
Ursane hybrids with 5-amino-1,2,3,4-thiatriazole, 1-tetrazole-5-thione, and 1-tetrazole-5-amines and study of their inhibition of main SARS-CoV-2 protease
inferred← citeshttps://doi.org/10.1016/j.synbio.2019.08.004openalex-snapshot
A novel D(−)-lactic acid-inducible promoter regulated by the GntR-family protein D-LldR of Pseudomonas fluorescens
inferred← citeshttps://doi.org/10.1016/j.taap.2019.03.014openalex-snapshot
Virtual screening-guided discovery of thioredoxin reductase inhibitors
inferred← citeshttps://doi.org/10.1016/j.tips.2020.10.005openalex-snapshot
Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors
inferred← citeshttps://doi.org/10.1016/j.trac.2024.117833openalex-snapshot
Advanced technologies for screening and identifying covalent inhibitors
inferred← citeshttps://doi.org/10.1016/j.trsl.2022.10.009openalex-snapshot
Targeting caspase-2 interactions with tau in Alzheimer's disease and related dementias
inferred← citeshttps://doi.org/10.1016/j.ymthe.2021.10.014openalex-snapshot
The neutralization effect of montelukast on SARS-CoV-2 is shown by multiscale in silico simulations and combined in vitro studies
inferred← citeshttps://doi.org/10.1021/acs.accounts.5c00905openalex-snapshot
Computational and AI-Driven Ecosystem for Structure-Based Covalent Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.biochem.2c00489openalex-snapshot
Predicting Antiviral Resistance Mutations in SARS-CoV-2 Main Protease with Computational and Experimental Screening
inferred← citeshttps://doi.org/10.1021/acs.biochem.7b01113openalex-snapshot
Design of Small Molecules That Compete with Nucleotide Binding to an Engineered Oncogenic KRAS Allele
inferred← citeshttps://doi.org/10.1021/acs.biochem.8b00178openalex-snapshot
Characterization of an A-Site Selective Protein Disulfide Isomerase A1 Inhibitor
inferred← citeshttps://doi.org/10.1021/acs.jafc.0c00835openalex-snapshot
Electron-Deficient Alkynes as Powerful Tools against Root-Knot Nematode Melodogyne incognita: Nematicidal Activity and Investigation on the Mode of Action
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.1c01278openalex-snapshot
Mechanism-Based and Computational-Driven Covalent Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00458openalex-snapshot
Discovery and Computational Studies of Potent Covalent Kinase Inhibitors with α-Substituent Electrophiles Targeting Cysteine
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c00693openalex-snapshot
Structure-Based Identification of Naphthoquinones and Derivatives as Novel Inhibitors of Main Protease M pro and Papain-like Protease PL pro of SARS-CoV-2
inferred← citeshttps://doi.org/10.1021/acs.jcim.2c01216openalex-snapshot
CovBinderInPDB: A Structure-Based Covalent Binder Database
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00061openalex-snapshot
MD-Based Assessment of Covalent Inhibitors in Noncovalent Association Complexes: Learning from Cathepsin K as a Test Case
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00127openalex-snapshot
Nonlocal Effects of Antibiotic-Resistance-Causing Mutations Reveal an Alternative Region for Targeting on FtsW–Penicillin-Binding Protein 3 Complex of Haemophilus influenzae
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00832openalex-snapshot
Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01055openalex-snapshot
Two-Step Covalent Docking with Attracting Cavities
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01900openalex-snapshot
Discovery of Covalent Lead Compounds Targeting 3CL Protease with a Lateral Interactions Spiking Neural Network
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00023openalex-snapshot
Computational Investigation of the Covalent Inhibition Mechanism of Bruton’s Tyrosine Kinase by Ibrutinib
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00418openalex-snapshot
Dynamics Playing a Key Role in the Covalent Binding of Inhibitors to Focal Adhesion Kinase
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01623openalex-snapshot
Development of Receptor Desolvation Scoring and Covalent Sampling in DOCK 6: Methods Evaluated on a RAS Test Set
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00201openalex-snapshot
Template-Based Docking Using Automated Maximum Common Substructure Identification with EnzyDock: Mechanistic and Inhibitor Docking
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00952openalex-snapshot
Kinetic Modeling of Covalent Inhibition: Effects of Rapidly Fluctuating Intermediate States
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c02496openalex-snapshot
Discovery of a Covalent Small-Molecule eEF1A1 Inhibitor via Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00334openalex-snapshot
Discovery of Covalent Ligands via Noncovalent Docking by Dissecting Covalent Docking Based on a “Steric-Clashes Alleviating Receptor (SCAR)” Strategy
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c02343openalex-snapshot
CHARMM-GUI Covalent Ligand Docker as a Web-Based Molecular Docking Platform for Covalent Ligands
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00163openalex-snapshot
Statistical Analysis and Prediction of Covalent Ligand Targeted Cysteine Residues
inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00228openalex-snapshot
Comparative Evaluation of Covalent Docking Tools
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00232openalex-snapshot
Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation
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