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Covalent docking using autodock: Two‐point attractor and flexible side chain methods
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1639::aid-jcc10>3.0.co;2-bopenalex-snapshot
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19991101)37:2<228::aid-prot8>3.0.co;2-8openalex-snapshot
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Characterization of Irreversible Kinase Inhibitors by Directly Detecting Covalent Bond Formation: A Tool for Dissecting Kinase Drug Resistance
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
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CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints
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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
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Improved protein–ligand docking using GOLD
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Drug discovery considerations in the development of covalent inhibitors
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Crystal Structures of Complexes between the R61 DD-peptidase and Peptidoglycan-mimetic β-Lactams: A Non-covalent Complex with a “Perfect Penicillin”
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Molecular modeling and crystal structure of ERK2–hypothemycin complexes
inferredcites →https://doi.org/10.1021/ci500118sopenalex-snapshot
Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring
inferredcites →https://doi.org/10.1021/ci500209eopenalex-snapshot
AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins
inferredcites →https://doi.org/10.1021/ci500681ropenalex-snapshot
DOCKTITE—A Highly Versatile Step-by-Step Workflow for Covalent Docking and Virtual Screening in the Molecular Operating Environment
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Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems
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A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking
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Covalent docking of large libraries for the discovery of chemical probes
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Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
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Strategies for Discovering and Derisking Covalent, Irreversible Enzyme Inhibitors
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Accelerating A uto D ock 4 with GPUs and Gradient-Based Local Search
inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00366openalex-snapshot
EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c01043openalex-snapshot
Rapid Solid-Phase Construction of Serine Hydrolase Probes Results in Selective Activity-Based Probes for Acyl Protein Thioesterases-1/2
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c02007openalex-snapshot
Cov_DOX: A Method for Structure Prediction of Covalent Protein–Ligand Bindings
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.2c01781openalex-snapshot
Insights into the Degradation of Polymer–Drug Conjugates by an Overexpressed Enzyme in Cancer Cells
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.3c00088openalex-snapshot
Rational Design of Covalent Kinase Inhibitors by an Integrated Computational Workflow (Kin-Cov)
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.3c01662openalex-snapshot
Design, Synthesis, and Evaluation of Cephamycin-Based Antisporulation Agents targeting Clostridioides difficile
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.3c02076openalex-snapshot
Reinvent Aliphatic Arsenicals as Reversible Covalent Warheads toward Targeted Kinase Inhibition and Non-acute Promyelocytic Leukemia Cancer Treatment
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c01947openalex-snapshot
Design, Synthesis, and Mechanism Study of Novel BMX Inhibitors Based on the Core of 1,3,5-Triazin-2-Amine for the Treatment of Gastric Carcinoma
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c02665openalex-snapshot
Orally Bioavailable and Site-Selective Covalent STING Inhibitor Derived from a Macrocyclic Marine Diterpenoid
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c02760openalex-snapshot
Covalent-Allosteric Inhibitors: Do We Get the Best of Both Worlds?
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5b02008openalex-snapshot
Docking Screens for Novel Ligands Conferring New Biology
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6b01413openalex-snapshot
Discovery of 2-((3-Acrylamido-4-methylphenyl)amino)-N-(2-methyl-5-(3,4,5-trimethoxybenzamido)phenyl)-4-(methylamino)pyrimidine-5-carboxamide (CHMFL-BMX-078) as a Highly Potent and Selective Type II Irreversible Bone Marrow Kinase in the X Chromosome (BMX) Kinase Inhibitor
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b00405openalex-snapshot
Development of Novel Peptide-Based Michael Acceptors Targeting Rhodesain and Falcipain-2 for the Treatment of Neglected Tropical Diseases (NTDs)
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00878openalex-snapshot
De Novo Design of Boron-Based Peptidomimetics as Potent Inhibitors of Human ClpP in the Presence of Human ClpX
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00908openalex-snapshot
Optimization Strategy of Novel Peptide-Based Michael Acceptors for the Treatment of Human African Trypanosomiasis
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b01879openalex-snapshot
Use of Non-Natural Amino Acids for the Design and Synthesis of a Selective, Cell-Permeable MALT1 Activity-Based Probe
inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c04710openalex-snapshot
Landscape of In Silico Tools for Modeling Covalent Modification of Proteins: A Review on Computational Covalent Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c02294openalex-snapshot
Papain-Mediated Conjugation of Peptide Nucleic Acids to Delivery Peptides: A Density Functional Theory/Molecular Mechanics Metadynamics Study in Aqueous and Organic Solvent
inferred← citeshttps://doi.org/10.1021/acschembio.0c00019openalex-snapshot
Integrative X-ray Structure and Molecular Modeling for the Rationalization of Procaspase-8 Inhibitor Potency and Selectivity
inferred← citeshttps://doi.org/10.1021/acschembio.4c00875openalex-snapshot
Discovery of IHMT-15130 as a Highly Potent Irreversible BMX Inhibitor for the Treatment of Myocardial Hypertrophy and Remodeling
inferred← citeshttps://doi.org/10.1021/acsinfecdis.3c00734openalex-snapshot
Potent Inhibition of E. coli DXP Synthase by a gem-Diaryl Bisubstrate Analog
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.0c00284openalex-snapshot
Facile Synthesis of Aminomethyl Phosphinate Esters as Serine Protease Inhibitors with Primed Site Interaction
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.3c00562openalex-snapshot
Identification of Dual Inhibitors Targeting Main Protease (M pro ) and Cathepsin L as Potential Anti-SARS-CoV-2 Agents
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.8b00477openalex-snapshot
L-DOPA-quinone Mediated Recovery from GIRK Channel Firing Inhibition in Dopaminergic Neurons
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.6c05137openalex-snapshot
Elucidating the Covalent Binding of Ottelione A and Withaferin A at the Colchicine Site of β-Tubulin
inferred← citeshttps://doi.org/10.1021/acsomega.8b03457openalex-snapshot
Simple Coordination Geometry Descriptors Allow to Accurately Predict Metal-Binding Sites in Proteins
inferred← citeshttps://doi.org/10.1021/acsptsci.3c00281openalex-snapshot
Structure-Based Identification of Kelch-like ECH-Associated Protein 1 as a Pharmacological Target of Electrophile-Containing Catechol-O-Methyltransferase Inhibitors
inferred← citeshttps://doi.org/10.1021/jacs.2c11098openalex-snapshot
Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence
inferred← citeshttps://doi.org/10.1021/jacs.5c05669openalex-snapshot
Inhibitor-Dependent Tolerance of New Delhi Metallo-β-Lactamase Driven by Single Mutation-Induced Conformational Changes
inferred← citeshttps://doi.org/10.1021/jacs.5c22222openalex-snapshot
Discovery of Covalent Ligands with AlphaFold3
inferred← citeshttps://doi.org/10.1021/jacs.9b10377openalex-snapshot
Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking
inferred← citeshttps://doi.org/10.1038/nprot.2016.051openalex-snapshot
Computational protein–ligand docking and virtual drug screening with the AutoDock suite
inferred← citeshttps://doi.org/10.1038/s41401-025-01721-5openalex-snapshot
Benchmarking co-folding methods to predict the structures of covalent protein–ligand complexes
inferred← citeshttps://doi.org/10.1038/s41429-025-00886-9openalex-snapshot
An atypical non-ribosomal peptide cyclase catalyzing homochiral coupling with cyclic amine nucleophile
inferred← citeshttps://doi.org/10.1038/s41467-018-02881-1openalex-snapshot
Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation
inferred← citeshttps://doi.org/10.1038/s41467-024-52574-1openalex-snapshot
Targeting a key protein-protein interaction surface on mitogen-activated protein kinases by a precision-guided warhead scaffold
inferred← citeshttps://doi.org/10.1038/s41467-026-74057-1openalex-snapshot
Genetic and pharmacological inactivation of peptidoglycan remodeling increases antibiotic susceptibility of vancomycin-resistant Enterococcus faecium
inferred← citeshttps://doi.org/10.1038/s41565-021-00872-wopenalex-snapshot
Extracellular vesicle drug occupancy enables real-time monitoring of targeted cancer therapy
inferred← citeshttps://doi.org/10.1038/s41586-021-04077-yopenalex-snapshot
Structure, function and pharmacology of human itch receptor complexes
inferred← citeshttps://doi.org/10.1038/s41586-022-04619-yopenalex-snapshot
Structural basis for the tethered peptide activation of adhesion GPCRs.
inferred← citeshttps://doi.org/10.1038/s41598-025-24614-3openalex-snapshot
Hybrid quantum/classical docking of covalent and non-covalent ligands with Attracting Cavities
inferred← citeshttps://doi.org/10.1038/s42004-025-01606-yopenalex-snapshot
Structure-based rational design of covalent probes
inferred← citeshttps://doi.org/10.1038/s44160-024-00671-wopenalex-snapshot
An engineered aldolase enables the biocatalytic synthesis of 2′-functionalized nucleoside analogues
inferred← citeshttps://doi.org/10.1038/s44298-024-00028-2openalex-snapshot
Study of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir
inferred← citeshttps://doi.org/10.1038/s44433-026-00009-6openalex-snapshot
Shikonin covalently binding to cysteine to inhibits the cleavage activity of the 3C-like serine main protease (Nsp4) of PRRSV-2 and suppresses viral replication in Marc-145 cells
inferred← citeshttps://doi.org/10.1039/9781839160745-00069openalex-snapshot
Best Practices for Design and Characterization of Covalent Chemical Probes
inferred← citeshttps://doi.org/10.1039/d0cb00222dopenalex-snapshot
Fragment-based covalent ligand discovery
inferred← citeshttps://doi.org/10.1039/d0qi01507eopenalex-snapshot
Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes
inferred← citeshttps://doi.org/10.1039/d1cp04159bopenalex-snapshot
Grammatical evolution-based design of SARS-CoV-2 main protease inhibitors
inferred← citeshttps://doi.org/10.1039/d2an00163bopenalex-snapshot
Sensitive sensing of alkaline phosphatase and γ-glutamyltranspeptidase activity for tumor imaging
inferred← citeshttps://doi.org/10.1039/d4dd00357hopenalex-snapshot
A workflow to create a high-quality protein–ligand binding dataset for training, validation, and prediction tasks
inferred← citeshttps://doi.org/10.1042/bst20180202openalex-snapshot
Protein structure and computational drug discovery
inferred← citeshttps://doi.org/10.1073/pnas.2535430123openalex-snapshot
Chemical neighborhood exploration for substrate discovery in biocatalysis
inferred← citeshttps://doi.org/10.1080/00387010.2023.2184833openalex-snapshot
Binding characteristics of Bruton’s tyrosine kinase inhibitor ibrutinib with bovine serum albumin: multi-spectroscopic combined with molecular simulation
inferred← citeshttps://doi.org/10.1080/07391102.2021.2007170openalex-snapshot
In silico screening and covalent binding of phytochemicals of Ocimum sanctum against SARS-CoV-2 (COVID 19) main protease
inferred← citeshttps://doi.org/10.1080/07391102.2023.2222839openalex-snapshot
In silico discovery of potent and selective Janus kinase 3 (JAK3) inhibitors through 3D-QSAR, covalent docking, ADMET analysis, molecular dynamics simulations, and binding free energy of pyrazolopyrimidine derivatives
inferred← citeshttps://doi.org/10.1080/07391102.2023.2270709openalex-snapshot
In silico computational drug discovery: a Monte Carlo approach for developing a novel JAK3 inhibitors
inferred← citeshttps://doi.org/10.1080/14756366.2020.1833876openalex-snapshot
Synthesis and biological activity of 2-cyanoacrylamide derivatives tethered to imidazopyridine as TAK1 inhibitors
inferred← citeshttps://doi.org/10.1085/jgp.202413559openalex-snapshot
Different fluorescent labels report distinct components of spHCN channel voltage sensor movement
inferred← citeshttps://doi.org/10.1093/bib/bbab301openalex-snapshot
A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe
inferred← citeshttps://doi.org/10.1093/bib/bbac559openalex-snapshot
HCovDock: an efficient docking method for modeling covalent protein–ligand interactions
inferred← citeshttps://doi.org/10.1093/bib/bbaf697openalex-snapshot
The covalent docking software landscape: features and applications in drug design
inferred← citeshttps://doi.org/10.1093/nar/gkab868openalex-snapshot
CovPDB: a high-resolution coverage of the covalent protein–ligand interactome
inferred← citeshttps://doi.org/10.1098/rsob.200050openalex-snapshot
Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer
inferred← citeshttps://doi.org/10.1101/2024.09.20.614087openalex-snapshot
A one-step protocol to generate impermeable fluorescent HaloTag substrates for in situ live cell application and super-resolution imaging
inferred← citeshttps://doi.org/10.1101/305243openalex-snapshot
Repurposing covalent EGFR/HER2 inhibitors for on-target degradation of human Tribbles 2 (TRIB2) pseudokinase
inferred← citeshttps://doi.org/10.1111/bph.15815openalex-snapshot
Peptidylglycine α‐amidating monooxygenase as a therapeutic target or biomarker for human diseases
inferred← citeshttps://doi.org/10.1111/cbdd.14184openalex-snapshot
An in silico comparative study of curcumin and 2‐deoxyuridine nucleoside derivatives: Reveals the role of angiogenin in ER stress‐induced apoptosis signaling
inferred← citeshttps://doi.org/10.1111/febs.70284openalex-snapshot
Exploring the influence of lid region residues on fatty acid selectivity in a lipase originating from Rhizopus oryzae
inferred← citeshttps://doi.org/10.11169/bioimages.29.11openalex-snapshot
In silico Design of Inhibitor Against SARS-CoV-2 Protease by Docking Simulation and ADMET Prediction
inferred← citeshttps://doi.org/10.1126/scisignal.aat7951openalex-snapshot
Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells
inferred← citeshttps://doi.org/10.1128/iai.00847-18openalex-snapshot
Structural and Functional Insights into PpgL, a Metal-Independent β-Propeller Gluconolactonase That Contributes to Pseudomonas aeruginosa Virulence
inferred← citeshttps://doi.org/10.1134/s1068162024030221openalex-snapshot
Novel Urea Substituted Benzimidazole Derivatives as Anthelmintics: In Silico and In Vitro Approaches
inferred← citeshttps://doi.org/10.1142/s0219633620400088openalex-snapshot
Xanthine oxidoreductase inhibition – A review of computational aspect
inferred← citeshttps://doi.org/10.1145/3711896.3736896openalex-snapshot
CovDocker: Benchmarking Covalent Drug Design with Tasks, Datasets, and Solutions
inferred← citeshttps://doi.org/10.1155/joch/9127169openalex-snapshot
Prospective Irreversible DprE1 Inhibitors for Tuberculosis: A Drug Repurposing Approach Using Covalent Docking and Molecular Dynamics
inferred← citeshttps://doi.org/10.1155/jotm/8879019openalex-snapshot
Exploring the Natural Products Atlas (NPAtlas) Database for Hunting Prospective Irreversible Covalent DprE1 Inhibitors With Antitubercular Activity: An Integrated In-Silico Approach
inferred← citeshttps://doi.org/10.1186/s12900-018-0092-5openalex-snapshot
Computational analysis of the interactions of a novel cephalosporin derivative with β-lactamases
inferred← citeshttps://doi.org/10.1186/s12929-024-01091-wopenalex-snapshot
Cyclophostin and Cyclipostins analogues counteract macrolide-induced resistance mediated by erm(41) in Mycobacterium abscessus
inferred← citeshttps://doi.org/10.1186/s12935-019-0773-6openalex-snapshot
WP1130 reveals USP24 as a novel target in T-cell acute lymphoblastic leukemia
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