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Applying molecular docking to pesticides

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Molecular docking towards drug discovery
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Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
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Gaussian docking functions
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Einfluss der Configuration auf die Wirkung der Enzyme
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Modeling Promiscuity Based on in vitro Safety Pharmacology Profiling Data
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Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm
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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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LigDockCSA: Protein–ligand docking using conformational space annealing
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GalaxyDock2: Protein–ligand docking using beta‐complex and global optimization
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DOCK 6: Impact of new features and current docking performance
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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
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Direct search methods for the molecular conformation problem
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Latest developments in molecular docking: 2010–2011 in review
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Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
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A Comparative Study on the Constitutive Properties of Marketed Pesticides
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Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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Improved protein–ligand docking using GOLD
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ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility
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Structure‐based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections
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FLIPDock: Docking flexible ligands into flexible receptors
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Flexible protein–flexible ligand docking with disrupted velocity simulated annealing
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A multiple‐start Monte Carlo docking method
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Gene amplification and insecticide resistance
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Towards the rational design of crop protection agents
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Perspectives on the agrochemical industry and agrochemical discovery
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Innovations in Agrochemical Discovery and the Role of Metabolism, Bioavailability and Formulations
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Impact of natural products on discovery of, and innovation in, crop protection compounds
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Machine‐learning scoring functions for structure‐based drug lead optimization
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Knowledge-based scoring function to predict protein-ligand interactions
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FlexE: efficient molecular docking considering protein structure variations
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Virtual Screening: An Alternative or Complement to High Throughput Screening?
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Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?
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Surflex-Dock: Docking benchmarks and real-world application
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Synthesis, Characterization, Biological Evaluation and Docking Study of Heterocyclic-Based Synthetic Sulfonamides as Potential Pesticide Against G. mellonella
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Software for molecular docking: a review
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ePlant for quantitative and predictive plant science research in the big data era —Lay the foundation for the future model guided crop breeding, engineering and agronomy
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Progress in molecular docking
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Docking-based inverse virtual screening: methods, applications, and challenges
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Pesticide informatics expands the opportunity for structure-based molecular design and optimization
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Discovery of novel A2AR antagonists through deep learning-based virtual screening
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The competitive binding between inhibitors and substrates of HCV NS3/4A protease: A general mechanism of drug resistance
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Bio-inspired optimization for the molecular docking problem: State of the art, recent results and perspectives
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Single and joint toxicity assessment of acetamiprid and thiamethoxam neonicotinoids pesticides on biochemical indices and antioxidant enzyme activities of a freshwater fish Catla catla
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The MCR-3 inside linker appears as a facilitator of colistin resistance
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The Process of Structure-Based Drug Design
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Molecular basis for the resistance of American sloughgrass to aryloxyphenoxypropionic acid pesticides and its environmental relevance: A combined experimental and computational study
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Exploring QSAR models for assessment of acute fish toxicity of environmental transformation products of pesticides (ETPPs)
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Carbofuran toxicity and its microbial degradation in contaminated environments
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Safeguarding production—losses in major crops and the role of crop protection
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Delineating the conformational landscape and intrinsic properties of the angiotensin II type 2 receptor using a computational study
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Essential considerations for using protein–ligand structures in drug discovery
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From machine learning to deep learning: progress in machine intelligence for rational drug discovery
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Machine learning in chemoinformatics and drug discovery
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Machine-learning methods for ligand–protein molecular docking
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Evaluation of modes of action of pesticides to Daphnia magna based on QSAR, excess toxicity and critical body residues
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Modeling pesticide residues in nectar and pollen in support of pesticide exposure assessment for honeybees: A generic modeling approach
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Toxicity of chemical pesticides commonly used in maize to Trichogramma ostriniae (Hymenoptera: Trichogrammatidae), an egg parasitoid of Asian corn borer
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Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review
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Effective adsorption of metolachlor herbicide by MIL-53(Al) metal-organic framework: Optimization, validation and molecular docking simulation studies
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Pesticide residues levels in raw cow's milk and health risk assessment across the globe: A systematic review
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The potential endocrine disruption of pesticide transformation products (TPs): The blind spot of pesticide risk assessment
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Pesticide resistance from historical agricultural chemical exposure in Thamnocephalus platyurus (Crustacea: Anostraca)
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QSAR analyses of organophosphates for insecticidal activity and its in-silico validation using molecular docking study
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Long–term monitoring of 155 multi–class pesticide residues in Indian vegetables and their risk assessment for consumer safety
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Octopamine Receptor Agonists Synergistically Increase the Selected Pesticides’ Toxicity in Rhopalosiphum Padi: Perspectives for Reducing Pesticide Use, Emergence of Resistant Strains and Environmental Impacts
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A study on the prevalence of heavy metals, pesticides, and microbial contaminants and antibiotics resistance pathogens in raw salad vegetables sold in Dhaka, Bangladesh
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Pesticide residues in drinking water, their potential risk to human health and removal options
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Computer-aided profiling of a unique broad-specific antibody and its application to an ultrasensitive fluoroimmunoassay for five N-methyl carbamate pesticides
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Reduced concentrations and toxicity of sediment-associated pesticides from vegetable planting field to surrounding waterways: Impacts of chemical properties and intrinsic toxicity
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Essential oils as an effective alternative for the treatment of COVID-19: Molecular interaction analysis of protease (Mpro) with pharmacokinetics and toxicological properties
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Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding
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eHiTS: A new fast, exhaustive flexible ligand docking system
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Application of reverse docking for target prediction of marine compounds with anti-tumor activity
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Discovery of novel HPPD inhibitors based on a combination strategy of pharmacophore, consensus docking and molecular dynamics
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Interaction of p53 with BRC analogs: A comparative design assisted by ZDOCK and CABS-Dock simulation
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Status of pesticide resistance and associated mutations in the two-spotted spider mite, Tetranychus urticae, in China
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Virtual screening based on pharmacophore model for developing novel HPPD inhibitors
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A new method for predicting the acute toxicity of carbamate pesticides based on the perspective of binding information with carrier protein
inferredcites →https://doi.org/10.1016/j.saa.2022.121503openalex-snapshot
Interaction of mancozeb with human hemoglobin: Spectroscopic, molecular docking and molecular dynamic simulation studies
inferredcites →https://doi.org/10.1016/j.sbi.2006.02.002openalex-snapshot
Flexible protein–protein docking
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Protein structure-based drug design: from docking to molecular dynamics
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Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
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Beware of docking!
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Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies
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Consensus scoring for ligand/protein interactions
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LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
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A new method for mapping macromolecular topography
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Lead discovery using molecular docking
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Synthesis and Insecticidal Activity Evaluation of Virtually Screened Phenylsulfonamides
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Structure Simplification of Natural Products as a Lead Generation Approach in Agrochemical Discovery
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Pesticide Informatics Platform (PIP): An International Platform for Pesticide Discovery, Residue, and Risk Evaluation
inferredcites →https://doi.org/10.1021/acs.jafc.6b03464openalex-snapshot
Design, Synthesis, Fungicidal Activity, and Unexpected Docking Model of the First Chiral Boscalid Analogues Containing Oxazolines
inferredcites →https://doi.org/10.1021/acs.jafc.8b06596openalex-snapshot
FungiPAD: A Free Web Tool for Compound Property Evaluation and Fungicide-Likeness Analysis
inferredcites →https://doi.org/10.1021/acs.jcim.1c00203openalex-snapshot
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
inferredcites →https://doi.org/10.1021/acs.jcim.5b00056openalex-snapshot
Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease
inferredcites →https://doi.org/10.1021/acs.jcim.8b00283openalex-snapshot
Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator
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PADFrag: A Database Built for the Exploration of Bioactive Fragment Space for Drug Discovery
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Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations
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InsectiPAD: A Web Tool Dedicated to Exploring Physicochemical Properties and Evaluating Insecticide-Likeness of Small Molecules
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Structural Diversity of Ligand-Binding Androgen Receptors Revealed by Microsecond Long Molecular Dynamics Simulations and Enhanced Sampling
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InteractionGraphNet: A Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein–Ligand Interaction Predictions
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Regulation Mechanism for the Binding between the SARS-CoV-2 Spike Protein and Host Angiotensin-Converting Enzyme II
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Deep Docking: A Deep Learning Platform for Augmentation of Structure Based Drug Discovery
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From Knowledge-Based Potentials to Combinatorial Lead Design in Silico
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Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions
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Virtual Screening for Ligands of the Insect Molting Hormone Receptor
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FRED Pose Prediction and Virtual Screening Accuracy
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Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening
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Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches
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Insight into Crizotinib Resistance Mechanisms Caused by Three Mutations in ALK Tyrosine Kinase using Free Energy Calculation Approaches
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Classification of Current Scoring Functions
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Docking Ligands into Flexible and Solvated Macromolecules. 1. Development and Validation of FITTED 1.0
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Validation Studies of the Site-Directed Docking Program LibDock
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GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein−Ligand Complexes
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Rational Design Based on Bioactive Conformation Analysis of Pyrimidinylbenzoates as Acetohydroxyacid Synthase Inhibitors by Integrating Molecular Docking, CoMFA, CoMSIA, and DFT Calculations
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Nucleophilic Aliphatic Substitution Reactions of Propachlor, Alachlor, and Metolachlor with Bisulfide (HS - ) and Polysulfides (S n 2 - )
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Computational Discovery of Picomolar Qo Site Inhibitors of Cytochrome bc1 Complex
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Structure-Based Design and Synthesis of Novel Dual-Target Inhibitors against Cyanobacterial Fructose-1,6-Bisphosphate Aldolase and Fructose-1,6-Bisphosphatase
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Photonucleophilic reactions of nitrofen
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China: Forward to the Green Pesticides via a Basic Research Program
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Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
inferredcites →https://doi.org/10.1021/jm0300173openalex-snapshot
Nuclear Hormone Receptor Targeted Virtual Screening
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
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A Critical Assessment of Docking Programs and Scoring Functions
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Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
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An open-source drug discovery platform enables ultra-large virtual screens
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Resistance Mechanisms and Molecular Docking Studies of Four Novel QoI Fungicides in Peronophythora litchii
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Integrated machine learning, molecular docking and 3D-QSAR based approach for identification of potential inhibitors of trypanosomal N -myristoyltransferase
inferredcites →https://doi.org/10.1039/d2cs00948jopenalex-snapshot
Surely you are joking, Mr Docking!
inferredcites →https://doi.org/10.1042/bj20020835openalex-snapshot
Triadimefon, a fungicidal triazole-type P450 inhibitor, induces brassinosteroid deficiency-like phenotypes in plants and binds to DWF4 protein in the brassinosteroid biosynthesis pathway
inferredcites →https://doi.org/10.1055/s-0043-125210openalex-snapshot
Molecular Docking Studies on Isocytosine Analogues as Xanthine Oxidase Inhibitors
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Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance
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Application of a Theory of Enzyme Specificity to Protein Synthesis
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Weighted Equation and Rules—A Novel Concept for Evaluating Protein-Ligand Interaction
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Using reverse docking for target identification and its applications for drug discovery
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TarFisDock: a web server for identifying drug targets with docking approach
inferredcites →https://doi.org/10.1093/nar/gks496openalex-snapshot
idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach
inferredcites →https://doi.org/10.1094/pdis-02-20-0393-reopenalex-snapshot
Survival Cost and Diverse Molecular Mechanisms of Magnaporthe oryzae Isolate Resistance to Epoxiconazole
inferredcites →https://doi.org/10.1094/pdis-08-19-1628-reopenalex-snapshot
Mutations and Overexpression of CYP51 Associated with DMI-Resistance in Colletotrichum gloeosporioides from Chili
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Detection and Biological Characteristics of Alternaria alternata Resistant to Difenoconazole from Paris polyphylla var. chinensis, an Indigenous Medicinal Herb
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Characterization of the Resistance Mechanism and Risk of Fusarium verticillioides to the Myosin Inhibitor Phenamacril
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Graph Learning: A Survey
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Recent developments in molecular docking technology applied in food science: a review
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Dynamic control of plant water use using designed ABA receptor agonists
inferredcites →https://doi.org/10.1186/1471-2105-12-s1-s33openalex-snapshot
iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis
inferredcites →https://doi.org/10.1186/1471-2164-13-6openalex-snapshot
RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
inferredcites →https://doi.org/10.1186/s12938-016-0272-0openalex-snapshot
Computer prediction of paratope on antithrombotic antibody 10B12 and epitope on platelet glycoprotein VI via molecular dynamics simulation
inferredcites →https://doi.org/10.1186/s13321-019-0394-zopenalex-snapshot
ACID: a free tool for drug repurposing using consensus inverse docking strategy
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inferredcites →https://doi.org/10.2174/156802608786786624openalex-snapshot
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inferredcites →https://doi.org/10.3389/fmicb.2017.00465openalex-snapshot
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inferredcites →https://doi.org/10.3389/fphar.2018.01089openalex-snapshot
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Pesticides in the Modern World - Risks and Benefits

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