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Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results

https://doi.org/10.1021/ci800420z
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What this work says

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

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Impact of Ligand Protonation on Virtual Screening against β-Secretase (BACE1)
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Computational Validation of the Importance of Absolute Stereochemistry in Virtual Screening
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Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS
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Tautomer Enumeration and Stability Prediction for Virtual Screening on Large Chemical Databases
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Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
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Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
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Virtual Screening Workflow Development Guided by the “Receiver Operating Characteristic” Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4
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Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
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Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase
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The Protein Data Bank
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Recent Advances in Docking and Scoring

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Virtual screening and zebrafish models in tandem, for drug discovery and development
inferred← citeshttps://doi.org/10.1088/1742-6596/1235/1/012053openalex-snapshot
Implementation of Microservices Architecture for Application of Cyclooxygenase-2 Inhibitors Identifier
inferred← citeshttps://doi.org/10.1093/bib/bbv037openalex-snapshot
Building a virtual ligand screening pipeline using free software: a survey
inferred← citeshttps://doi.org/10.1093/nar/gkae326openalex-snapshot
ChemoDOTS: a web server to design chemistry-driven focused libraries
inferred← citeshttps://doi.org/10.1096/fj.201900945ropenalex-snapshot
Cyanidin‐3‐glucoside binds to talin and modulates colon cancer cell adhesions and 3D growth
inferred← citeshttps://doi.org/10.1101/2022.05.20.492762openalex-snapshot
Rudimentary Structure-Activity-Relationship study of the MMV Pathogen Box compound MMV675968 (2,4-diaminoquinazoline) unveils novel inhibitors of Trypanosoma brucei brucei DHFR enzyme
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/10.1155/2024/5583526openalex-snapshot
Structure Identification and Risk Assurance of Unknown Impurities in Pramipexole Oral Drug Formulation
inferred← citeshttps://doi.org/10.11606/d.9.2021.tde-05082021-002930openalex-snapshot
Reposicionamento de fármacos para o tratamento da doença de Chagas: desenvolvimento de modelos computacionais baseados em ligantes ativos fenotipicamente contra o >i /i< e na inibição da diidroorotato desidrog
inferred← citeshttps://doi.org/10.1186/1472-6807-12-21openalex-snapshot
Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)
inferred← citeshttps://doi.org/10.1186/1758-2946-2-s1-p43openalex-snapshot
A combined combinatorial and pKa-based approach to ligand protonation states
inferred← citeshttps://doi.org/10.1186/s12859-025-06120-5openalex-snapshot
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures
inferred← citeshttps://doi.org/10.1186/s13321-015-0074-6openalex-snapshot
Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization
inferred← citeshttps://doi.org/10.12691/ajmo-2-4-1openalex-snapshot
Some Critical Aspects of Molecular Interactions Between Drugs and Receptors
inferred← citeshttps://doi.org/10.12691/ajmo-3-3-2openalex-snapshot
How Important is to Account for Water When Modeling Biomolecular Complexes
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004018openalex-snapshot
Protein-Protein Docking with Dynamic Residue Protonation States
inferred← citeshttps://doi.org/10.1371/journal.pntd.0010545openalex-snapshot
In silico investigation of cytochrome bc1 molecular inhibition mechanism against Trypanosoma cruzi
inferred← citeshttps://doi.org/10.1371/journal.pone.0318712openalex-snapshot
Evaluating the structure-based virtual screening performance of SARS-CoV-2 main protease: A benchmarking approach and a multistage screening example against the wild-type and Omicron variants
inferred← citeshttps://doi.org/10.14499/indonesianjpharm26iss1pp20openalex-snapshot
CONSTRUCTION AND RETROSPECTIVE VALIDATION OF STRUCTURE-BASED VIRTUAL SCREENING PROTOCOLS TO IDENTIFY POTENT LIGANDS FOR HUMAN ADRENERGIC BETA-2 RECEPTOR
inferred← citeshttps://doi.org/10.14499/indonesianjpharm27iss3pp163openalex-snapshot
OPTIMIZING STRUCTURE-BASED VIRTUAL SCREENING PROTOCOL TO IDENTIFY PHYTOCHEMICALS AS CYCLOOXYGENASE-2 INHIBITORS
inferred← citeshttps://doi.org/10.14499/indonesianjpharm28iss2pp100openalex-snapshot
Computer-aided Design of Chalcone Derivatives as Lead Compounds Targeting Acetylcholinesterase
inferred← citeshttps://doi.org/10.1517/17460441.2010.484460openalex-snapshot
Virtual screening with AutoDock: theory and practice
inferred← citeshttps://doi.org/10.1590/s2175-97902025e24064openalex-snapshot
Molecular docking and quantitative structure-activity relationships for a series of Trypanosoma cruzi dihydroorotate dehydrogenase inhibitors
inferred← citeshttps://doi.org/10.21203/rs.3.rs-10753552/v1openalex-snapshot
Prospects for the use of 3-R-benzo[f][1,2,4]triazino[2,3-d][1,4]diazepine-2,7(6H,8H)-diones as agonists and antagonists of GABAA receptors
inferred← citeshttps://doi.org/10.21203/rs.3.rs-10753552/v2openalex-snapshot
Prospects for the use of 3-R-benzo[f][1,2,4]triazino[2,3-d][1,4]diazepine-2,7(6H,8H)-diones as agonists and antagonists of GABAA receptors
inferred← citeshttps://doi.org/10.2147/dddt.s537065openalex-snapshot
Benchmarking the Structure-Based Virtual Screening Performance of Wild-Type and Resistant PfDHFR Using Docking and Machine Learning Re-Scoring
inferred← citeshttps://doi.org/10.21577/0100-4042.20230038openalex-snapshot
MACHINE LEARNING-BASED VIRTUAL SCREENING, MOLECULAR DOCKING, DRUG-LIKENESS, PHARMACOKINETICS AND TOXICITY ANALYSES TO IDENTIFY NEW NATURAL INHIBITORS OF THE GLYCOPROTEIN SPIKE (S1) OF SARS-CoV-2
inferred← citeshttps://doi.org/10.2174/0118715206299644240523054454openalex-snapshot
The Importance of Structural Water in HDAC8 for Correct Binding Pose Applied for Drug Design of Anticancer Molecules
inferred← citeshttps://doi.org/10.2174/0929867326666190614160451openalex-snapshot
VSPrep: A KNIME Workflow for the Preparation of Molecular Databases for Virtual Screening
inferred← citeshttps://doi.org/10.2174/1381612811319230004openalex-snapshot
The Role of Protonation States in Ligand-Receptor Recognition and Binding
inferred← citeshttps://doi.org/10.2174/1386207322666190705143322openalex-snapshot
Molecular Docking Supplements an In vitro Determination of the Leading CYP Isoform for Arylpiperazine Derivatives
inferred← citeshttps://doi.org/10.2174/1573406412666160404125718openalex-snapshot
Synthesis of 1,4-disubstituted 1,2,3-triazole Derivatives Using Click Chemistry and their Src Kinase Activities
inferred← citeshttps://doi.org/10.2174/157340911795677602openalex-snapshot
Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery
inferred← citeshttps://doi.org/10.2174/978160805142711101010099openalex-snapshot
Receptor Flexibility in Ligand Docking and Virtual Screening
inferred← citeshttps://doi.org/10.22146/ijc.24172openalex-snapshot
Binary Quantitative Structure-Activity Relationship Analysis to Increase the Predictive Ability of Structure-Based Virtual Screening Campaigns Targeting Cyclooxygenase-2
inferred← citeshttps://doi.org/10.22146/ijc.34561openalex-snapshot
Development of a Graphical User Interface Application to Identify Marginal and Potent Ligands for Estrogen Receptor Alpha
inferred← citeshttps://doi.org/10.22146/ijc.50674openalex-snapshot
Docking-Guided 3D-QSAR Studies of 4-Aminoquinoline-1,3,5-triazines as Inhibitors for Plasmodium falciparum Dihydrofolate Reductase
inferred← citeshttps://doi.org/10.22146/ijc.55447openalex-snapshot
Computer-Aided Discovery of Pentapeptide AEYTR as a Potent Acetylcholinesterase Inhibitor
inferred← citeshttps://doi.org/10.22159/ajpcr.2017.v10i12.20667openalex-snapshot
BINARY QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP ANALYSIS IN RETROSPECTIVE STRUCTURE-BASED VIRTUAL SCREENING CAMPAIGNS TARGETING ESTROGEN RECEPTOR ALPHA
inferred← citeshttps://doi.org/10.22159/ijap.2022v14i4.44631openalex-snapshot
MOLECULAR DYNAMICS SIMULATIONS OF THE CAFFEIC ACID INTERACTIONS TO DIPEPTIDYL PEPTIDASE IV
inferred← citeshttps://doi.org/10.22487/j24428744.2021.v7.i2.15516openalex-snapshot
Identification of Interactions of ABT-341 to Dipeptidyl Peptidase IV during Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.24071/jpsc.142698openalex-snapshot
VIRTUAL SCREENING CAMPAIGNS ON ISOFLAVONES TO DISCOVER POTENT CYCLOOXYGENASE-2 INHIBITORS
inferred← citeshttps://doi.org/10.2991/iccst-15.2015.23openalex-snapshot
Cembranoid Diterpenes as Antitumor: Molecular Docking Study to Several Protein Receptor Targets
inferred← citeshttps://doi.org/10.3389/fchem.2018.00043openalex-snapshot
An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings
inferred← citeshttps://doi.org/10.3389/fchem.2020.00343openalex-snapshot
Structure-Based Virtual Screening: From Classical to Artificial Intelligence
inferred← citeshttps://doi.org/10.3389/fphar.2023.1129997openalex-snapshot
In-silico studies to recognize repurposing therapeutics toward arginase-I inhibitors as a potential onco-immunomodulators
inferred← citeshttps://doi.org/10.3390/biom16050724openalex-snapshot
Evaluation of 3′,4′-Di-O-acetyl-cis-khellactone as a Putative Antagonist of PPARγ Using Experimental and Computational Modeling
inferred← citeshttps://doi.org/10.3390/cancers18050719openalex-snapshot
Artificial Intelligence-Driven Natural Product Discovery for Cancer Metastasis and Chemoresistance: From Computational Prediction to Preclinical Validation
inferred← citeshttps://doi.org/10.3390/computation12050094openalex-snapshot
To Bind or Not to Bind? A Comprehensive Characterization of TIR1 and Auxins Using Consensus In Silico Approaches
inferred← citeshttps://doi.org/10.3390/ijms22115807openalex-snapshot
VirtualFlow Ants—Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization
inferred← citeshttps://doi.org/10.3390/ijms23031906openalex-snapshot
Identification of Corosolic and Oleanolic Acids as Molecules Antagonizing the Human RORγT Nuclear Receptor Using the Calculated Fingerprints of the Molecular Similarity
inferred← citeshttps://doi.org/10.3390/ijms25010552openalex-snapshot
Exploring the Mechanism of Activation of CFTR by Curcuminoids: An Ensemble Docking Study
inferred← citeshttps://doi.org/10.3390/ijms27073302openalex-snapshot
Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities
inferred← citeshttps://doi.org/10.3390/life13081739openalex-snapshot
Structure-Based Multi-Targeted Molecular Docking and Dynamic Simulation of Soybean-Derived Isoflavone Genistin as a Potential Breast Cancer Signaling Proteins Inhibitor
inferred← citeshttps://doi.org/10.3390/molecules26092452openalex-snapshot
PyPLIF HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors
inferred← citeshttps://doi.org/10.3390/molecules27175661openalex-snapshot
PyPLIF HIPPOS and Receptor Ensemble Docking Increase the Prediction Accuracy of the Structure-Based Virtual Screening Protocol Targeting Acetylcholinesterase
inferred← citeshttps://doi.org/10.3390/molecules27196574openalex-snapshot
Preliminary Structure–Activity Relationship Study of the MMV Pathogen Box Compound MMV675968 (2,4-Diaminoquinazoline) Unveils Novel Inhibitors of Trypanosoma brucei brucei
inferred← citeshttps://doi.org/10.3390/molecules28031296openalex-snapshot
In Silico Targeting of Fascin Protein for Cancer Therapy: Benchmarking, Virtual Screening and Molecular Dynamics Approaches
inferred← citeshttps://doi.org/10.3390/ph18070982openalex-snapshot
A New In Silico Comparison of the Relative Affinity of Enantiomeric Chloroquine (CQ) and Hydroxychloroquine (HCQ) for ACE2
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch008openalex-snapshot
Protein-Ligand Docking Methodologies and Its Application in Drug Discovery
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch035openalex-snapshot
Protein-Ligand Docking Methodologies and Its Application in Drug Discovery
inferred← citeshttps://doi.org/10.5114/bta.2011.46542openalex-snapshot
REVIEW PAPER Virtual screening strategies in drug design – methods and applications
inferred← citeshttps://doi.org/10.52711/2231-5691.2024.00053openalex-snapshot
An Overview of Molecular Docking
inferred← citeshttps://doi.org/10.5935/1984-6835.20120055openalex-snapshot
Virtual Screening Strategies in Drug Design
inferred← citeshttps://doi.org/10.6026/97320630008901openalex-snapshot
Structure-based design of eugenol analogs as potential estrogen receptor antagonists
inferred← citeshttps://doi.org/10.64898/2026.04.24.720584openalex-snapshot
Dibenzoylmethane, a novel β-diketone pore blocker of large-conductance calcium-activated potassium channel
inferred← citeshttps://doi.org/10.70675/c04eeb3az351fz48ddza731z6ad3d5044e23openalex-snapshot
Développement d'outils de chémoinformatique pour l'identification d'inhibiteurs de protéines kinases à partir de fragments
inferred← citeshttps://doi.org/10.7324/japs.2019.90903openalex-snapshot
Comparison of dopamine D2 receptor (homology model and X-ray structure) and virtual screening protocol validation for the antagonism mechanism
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