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How to Improve Docking Accuracy of AutoDock4.2: A Case Study Using Different Electrostatic Potentials
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
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Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
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Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Flexible ligand docking: A multistep strategy approach
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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
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Automated docking of flexible ligands: Applications of autodock
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Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation
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UCSF Chimera—A visualization system for exploratory research and analysis
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A semiempirical free energy force field with charge‐based desolvation
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
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VoteDock: Consensus docking method for prediction of protein–ligand interactions
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Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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ZDOCK: An initial‐stage protein‐docking algorithm
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Improved protein–ligand docking using GOLD
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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
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Comparative evaluation of eight docking tools for docking and virtual screening accuracy
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Protein–ligand docking: Current status and future challenges
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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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Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
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Sur les r�les respectifs des �lectrons ? et ? dans les propri�t�s des d�riv�s halog�n�s des mol�cules conjugu�es. Application � l'�tude de l'uracile et du fluorouracile
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Development and validation of a modular, extensible docking program: DOCK 5
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Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
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Electronic structure of the α-amino acids of proteins
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A geometric approach to macromolecule-ligand interactions
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Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges
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The effect of different electrostatic potentials on docking accuracy: A case study using DOCK5.4
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The consequences of scoring docked ligand conformations using free energy correlations
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A new model for calculating atomic charges in molecules
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ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
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An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein−Ligand Complexes
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How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein–Protein Interfaces?
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Evaluations of Molecular Docking Programs for Virtual Screening
inferredcites →https://doi.org/10.1021/ci800063vopenalex-snapshot
Molecular Docking of Intercalators and Groove-Binders to Nucleic Acids Using Autodock and Surflex
inferredcites →https://doi.org/10.1021/ci900345hopenalex-snapshot
Ligand−Protein Cross-Docking with Water Molecules
inferredcites →https://doi.org/10.1021/ja00346a026openalex-snapshot
Electronegativity and bond energy
inferredcites →https://doi.org/10.1021/je60033a020openalex-snapshot
A brief review and table of semiempirical parameters used in the Hueckel molecular orbital method
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot
Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
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/jm048957qopenalex-snapshot
The PDBbind Database: Methodologies and Updates
inferredcites →https://doi.org/10.1021/jm050543popenalex-snapshot
Modeling Water Molecules in Protein−Ligand Docking Using GOLD
inferredcites →https://doi.org/10.1021/jp710169mopenalex-snapshot
Assessing the Role of Polarization in Docking
inferredcites →https://doi.org/10.1021/jp9717655openalex-snapshot
Application of the RESP Methodology in the Parametrization of Organic Solvents
inferredcites →https://doi.org/10.1038/nature05981openalex-snapshot
Structure-based activity prediction for an enzyme of unknown function
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812. A simple MO–LCAO method for the calculation of charge distributions in saturated organic molecules
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Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.1186/1758-2946-1-15openalex-snapshot
Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock
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inferred← citeshttps://doi.org/10.1080/07391102.2017.1414634openalex-snapshot
Understanding the interactions of different substrates with wild-type and mutant acylaminoacyl peptidase using molecular dynamics simulations
inferred← citeshttps://doi.org/10.1080/07391102.2018.1438921openalex-snapshot
Investigation of the selectivity of one type of small-molecule inhibitor for three Nav channel isoforms based on the method of computer simulation
inferred← citeshttps://doi.org/10.1080/07391102.2020.1824811openalex-snapshot
Dihydroartemisinin as a potential drug candidate for cancer therapy: a structural-based virtual screening for multitarget profiling
inferred← citeshttps://doi.org/10.1080/07391102.2021.1925156openalex-snapshot
Structural characterization of cassava linamarase-linamarin enzyme complex: an integrated computational approach
inferred← citeshttps://doi.org/10.1080/07391102.2024.2308762openalex-snapshot
An ensemble docking-based virtual screening and molecular dynamics simulation of phytochemical compounds from Malaysian Kelulut Honey (KH) against SARS-CoV-2 target enzyme, human angiotensin-converting enzyme 2 (ACE-2)
inferred← citeshttps://doi.org/10.1080/10286020.2024.2402369openalex-snapshot
Study on the anti-HBV activity of matrine alkaloids from Oxytropis ochrocephala by MTT, 3d-QSAR, molecular docking and molecular dynamics simulation
inferred← citeshttps://doi.org/10.1080/10406638.2024.2408461openalex-snapshot
QSAR Modeling, Molecular Docking and ADMET Study of Aryl Fluorosulfate Derivatives as Potential Anti-TB Agents
inferred← citeshttps://doi.org/10.1080/10739149.2015.1105817openalex-snapshot
Characterization of the interaction between bovine serum albumin and doxycycline by chemiluminescence and molecular docking
inferred← citeshttps://doi.org/10.1080/21691401.2026.2726112openalex-snapshot
Network pharmacology, and molecular docking studies for two flavonoid compounds isolated from Dodonaea viscosa towards SARS-CoV-2 infection and loaded in lipid nanoparticles
inferred← citeshttps://doi.org/10.1111/cbdd.13425openalex-snapshot
Design, synthesis, and biological evaluation of thieno[3,2‐d]pyrimidine derivatives as potential simplified phosphatidylinositol 3‐kinase alpha inhibitors
inferred← citeshttps://doi.org/10.1134/s1062359023604366openalex-snapshot
Genotoxic, Biochemical and Morphotoxic Assessment of Dimethoate: Ameliorative Role of Grape Seed (Vitis vinifera L.) Extract
inferred← citeshttps://doi.org/10.1155/2019/4982062openalex-snapshot
Identification of Chinese Herbal Compounds with Potential as JAK3 Inhibitors
inferred← citeshttps://doi.org/10.1186/1476-4598-12-135openalex-snapshot
6-Shogaol induces apoptosis in human leukemia cells through a process involving caspase-mediated cleavage of eIF2α
inferred← citeshttps://doi.org/10.13005/bbra/2962openalex-snapshot
In-silico Studies of Thiopyridine Compounds as Anti-Bacterial agents Targeting Enoyl - Acyl Carrier Protein Reductase
inferred← citeshttps://doi.org/10.1371/journal.pone.0313094openalex-snapshot
Targeting necroptosis in MCF-7 breast cancer cells: In Silico insights into 8,12-dimethoxysanguinarine from Eomecon Chionantha through molecular docking, dynamics, DFT, and MEP studies
inferred← citeshttps://doi.org/10.14710/jksa.26.7.238-248openalex-snapshot
Synthesis and Computational Study of Bis-(1-(3-Chlorobenzoyl)-3-Phenylthiourea) Cobalt (III) as Anticancer Candidate
inferred← citeshttps://doi.org/10.1590/fst.68722openalex-snapshot
Preparation and characterization of an oridonin and γ-cyclodextrin complex
inferred← citeshttps://doi.org/10.1590/s1984-29612020036openalex-snapshot
Anti-tick effect and cholinesterase inhibition caused by Prosopis juliflora alkaloids: in vitro and in silico studies
inferred← citeshttps://doi.org/10.21203/rs.3.rs-1537951/v1openalex-snapshot
CFTR, one membrane protein, inhibits proliferation and metastasis of hepatocellular carcinoma through new pathways
inferred← citeshttps://doi.org/10.21315/mjms2020.27.6.5openalex-snapshot
Hypolipidaemic and Insulin Secretagogue Activities of (R)-(−)-Carvone
inferred← citeshttps://doi.org/10.2174/0109298665333333240909104354openalex-snapshot
Investigating In silico and In vitro Therapeutic Potential of Diosmetin as the Anti-Parkinson Agent
inferred← citeshttps://doi.org/10.2174/1574893615666191219094216openalex-snapshot
Relevance of Molecular Docking Studies in Drug Designing
inferred← citeshttps://doi.org/10.3136/fstr.27.735openalex-snapshot
High-efficiency formation mechanism of mangiferin/γ-cyclodextrin complex
inferred← citeshttps://doi.org/10.32604/biocell.2021.015530openalex-snapshot
PPARγ LBD and its ligand specificity reveal a selection of potential partial agonist: Molecular dynamics based T2D drug discovery initiative
inferred← citeshttps://doi.org/10.3389/fchem.2020.595097openalex-snapshot
In Silico Study of Coumarins and Quinolines Derivatives as Potent Inhibitors of SARS-CoV-2 Main Protease
inferred← citeshttps://doi.org/10.3389/fphar.2022.870848openalex-snapshot
Sodium Tanshinone IIA Sulfonate as a Potent IDO1/TDO2 Dual Inhibitor Enhances Anti-PD1 Therapy for Colorectal Cancer in Mice
inferred← citeshttps://doi.org/10.3390/app14135549openalex-snapshot
Glycine-Conjugated α-Mangostins as Potential Estrogen Receptor Alpha (ERα) Antagonists through Pharmacophore Modeling, Docking Analysis, and Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.3390/app15031493openalex-snapshot
Revitalizing Recovery: Unveiling the Potential of Apigenin and Related Flavonoids in Long COVID-19 Therapy Through Molecular Dynamics Simulation
inferred← citeshttps://doi.org/10.3390/biophysica4020013openalex-snapshot
Deciphering the Molecular Interaction Process of Gallium Maltolate on SARS-CoV-2 Main and Papain-Like Proteases: A Theoretical Study
inferred← citeshttps://doi.org/10.3390/foods11223724openalex-snapshot
Encapsulation of Benzyl Isothiocyanate with β-Cyclodextrin Using Ultrasonication: Preparation, Characterization, and Antibacterial Assay
inferred← citeshttps://doi.org/10.3390/ijms150610459openalex-snapshot
Computational Study on Substrate Specificity of a Novel Cysteine Protease 1 Precursor from Zea mays
inferred← citeshttps://doi.org/10.3390/ijms22073413openalex-snapshot
5-O-methylcneorumchromone K Exerts Antinociceptive Effects in Mice via Interaction with GABAA Receptors
inferred← citeshttps://doi.org/10.3390/ijms23052564openalex-snapshot
Reorienting Mechanism of Harderoheme in Coproheme Decarboxylase—A Computational Study
inferred← citeshttps://doi.org/10.3390/ijms262010187openalex-snapshot
Rational Engineering of Patchoulene Synthase from Pogostemon cablin for Enhanced Patchoulene Production
inferred← citeshttps://doi.org/10.3390/ijms27083630openalex-snapshot
Structural Characterization, Toxicity Assessment and Molecular Modeling of Forced Degradation Products of Siponimod
inferred← citeshttps://doi.org/10.3390/molecules27051655openalex-snapshot
Rational Design and Synthesis of HSF1-PROTACs for Anticancer Drug Development
inferred← citeshttps://doi.org/10.3390/molecules28114458openalex-snapshot
Design, Synthesis and Biological Evaluation of α-Synuclein Proteolysis-Targeting Chimeras
inferred← citeshttps://doi.org/10.3390/molecules29174203openalex-snapshot
Exploring Radioiodinated Anastrozole and Epirubicin as AKT1-Targeted Radiopharmaceuticals in Breast Cancer: In Silico Analysis and Potential Therapeutic Effect with Functional Nuclear Imagining Implications
inferred← citeshttps://doi.org/10.3390/ph18081241openalex-snapshot
Network Pharmacology and Experimental Validation Identify Paeoniflorin as a Novel SRC-Targeted Therapy for Castration-Resistant Prostate Cancer
inferred← citeshttps://doi.org/10.3390/pharmaceutics13111776openalex-snapshot
Development of Mitomycin C-Loaded Nanoparticles Prepared Using the Micellar Assembly Driven by the Combined Effect of Hydrogen Bonding and π–π Stacking and Its Therapeutic Application in Bladder Cancer
inferred← citeshttps://doi.org/10.3390/pr12061177openalex-snapshot
Identification and Absorption–Distribution–Metabolism–Excretion–Toxicity Prediction of Potential MTHFD2 Enzyme Inhibitors from Urtica dioica Ethanolic Leaf Extract
inferred← citeshttps://doi.org/10.3390/pr9010071openalex-snapshot
Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development
inferred← citeshttps://doi.org/10.34172/ps.025.40914openalex-snapshot
Phytosterol Glycosides from Olaxsubscorpioidea Oliv. Exhibit Cytotoxic Effects in InVitro and InSilico Studies
inferred← citeshttps://doi.org/10.38186/difcie.58.03openalex-snapshot
Métodos computacionales para estimar la afinidad de un complejo ligando-receptor
inferred← citeshttps://doi.org/10.4018/978-1-5225-0362-0.ch003openalex-snapshot
Molecular Docking Challenges and Limitations
inferred← citeshttps://doi.org/10.4018/978-1-5225-1762-7.ch030openalex-snapshot
Molecular Docking Challenges and Limitations
inferred← citeshttps://doi.org/10.4236/jbm.2025.138013openalex-snapshot
Computational Insights into Moxifloxacin Resistance Conferred in Asn499 Mutants of Mycobacterium tuberculosis DNA Gyrase
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