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Lessons Learned from Molecular Scaffold Analysis
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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“Scaffold-Hopping” by Topological Pharmacophore Search: A Contribution to Virtual Screening
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Drug Design Strategies for Targeting G-Protein-Coupled Receptors
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A Scaffold‐Tree‐Merging Strategy for Prospective Bioactivity Annotation of γ‐Pyrones
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Scaffold Distributions in Bioactive Molecules, Clinical Trials Compounds, and Drugs
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Structural and Potency Relationships between Scaffolds of Compounds Active against Human Targets
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Rational approaches to targeted polypharmacology: creating and navigating protein–ligand interaction networks
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Drugs in other drugs: a new look at drugs as fragments
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A chemogenomic approach to drug discovery: focus on cardiovascular diseases
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Selection of heterocycles for drug design
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Chemical substructures in drug discovery
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Medicinal chemistry of target family-directed masterkeys
inferredcites →https://doi.org/10.1021/cc990047kopenalex-snapshot
Definition of Templates within Combinatorial Libraries
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Algorithm for Naming Molecular Equivalence Classes Represented by Labeled Pseudographs
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Is There a Difference between Leads and Drugs? A Historical Perspective
inferredcites →https://doi.org/10.1021/ci025535lopenalex-snapshot
Using Molecular Equivalence Numbers To Visually Explore Structural Features that Distinguish Chemical Libraries
inferredcites →https://doi.org/10.1021/ci0400213openalex-snapshot
Information Content in Organic Molecules: Quantification and Statistical Structure via Brownian Processing
inferredcites →https://doi.org/10.1021/ci049714+openalex-snapshot
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening
inferredcites →https://doi.org/10.1021/ci049744copenalex-snapshot
Generalized Fragment-Substructure Based Property Prediction Method
inferredcites →https://doi.org/10.1021/ci050352vopenalex-snapshot
Assessing the Scaffold Diversity of Screening Libraries
inferredcites →https://doi.org/10.1021/ci060117sopenalex-snapshot
On Outliers and Activity CliffsWhy QSAR Often Disappoints
inferredcites →https://doi.org/10.1021/ci100059qopenalex-snapshot
Molecular Scaffolds with High Propensity to Form Multi-Target Activity Cliffs
inferredcites →https://doi.org/10.1021/ci100203eopenalex-snapshot
Compound Set Enrichment: A Novel Approach to Analysis of Primary HTS Data
inferredcites →https://doi.org/10.1021/ci1003637openalex-snapshot
Polypharmacology Directed Compound Data Mining: Identification of Promiscuous Chemotypes with Different Activity Profiles and Comparison to Approved Drugs
inferredcites →https://doi.org/10.1021/ci100448aopenalex-snapshot
Combining Horizontal and Vertical Substructure Relationships in Scaffold Hierarchies for Activity Prediction
inferredcites →https://doi.org/10.1021/ci2000924openalex-snapshot
Mining for Bioactive Scaffolds with Scaffold Networks: Improved Compound Set Enrichment from Primary Screening Data
inferredcites →https://doi.org/10.1021/ci600338xopenalex-snapshot
The Scaffold Tree − Visualization of the Scaffold Universe by Hierarchical Scaffold Classification
inferredcites →https://doi.org/10.1021/ci700108qopenalex-snapshot
Mining of Randomly Generated Molecular Fragment Populations Uncovers Activity-Specific Fragment Hierarchies
inferredcites →https://doi.org/10.1021/ci7003412openalex-snapshot
Scaffold Topologies. 1. Exhaustive Enumeration up to Eight Rings
inferredcites →https://doi.org/10.1021/ci700342hopenalex-snapshot
Scaffold Topologies. 2. Analysis of Chemical Databases
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PubChem as a Source of Polypharmacology
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Drug and Drug Candidate Building Block Analysis
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Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation
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RECAPRetrosynthetic Combinatorial Analysis Procedure: A Powerful New Technique for Identifying Privileged Molecular Fragments with Useful Applications in Combinatorial Chemistry
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970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13
inferredcites →https://doi.org/10.1021/jm00120a002openalex-snapshot
Methods for drug discovery: development of potent, selective, orally effective cholecystokinin antagonists
inferredcites →https://doi.org/10.1021/jm049032dopenalex-snapshot
HierS: Hierarchical Scaffold Clustering Using Topological Chemical Graphs
inferredcites →https://doi.org/10.1021/jm0502900openalex-snapshot
Are Target-Family-Privileged Substructures Truly Privileged?
inferredcites →https://doi.org/10.1021/jm060217popenalex-snapshot
Quest for the Rings. In Silico Exploration of Ring Universe To Identify Novel Bioactive Heteroaromatic Scaffolds
inferredcites →https://doi.org/10.1021/jm100933wopenalex-snapshot
Activity Landscape Representations for Structure−Activity Relationship Analysis
inferredcites →https://doi.org/10.1021/jm701021bopenalex-snapshot
Kinase-likeness and Kinase-Privileged Fragments: Toward Virtual Polypharmacology
inferredcites →https://doi.org/10.1021/jm701399fopenalex-snapshot
Chemical Fragments as Foundations for Understanding Target Space and Activity Prediction
inferredcites →https://doi.org/10.1021/jm8000373openalex-snapshot
Recent Developments in Fragment-Based Drug Discovery
inferredcites →https://doi.org/10.1021/jm900075gopenalex-snapshot
Pyranonaphthoquinone Lactones: A New Class of AKT Selective Kinase Inhibitors Alkylate a Regulatory Loop Cysteine
inferredcites →https://doi.org/10.1021/jm901132vopenalex-snapshot
Selectively Nonselective Kinase Inhibition: Striking the Right Balance
inferredcites →https://doi.org/10.1021/jm9014229openalex-snapshot
Systematic Analysis of Public Domain Compound Potency Data Identifies Selective Molecular Scaffolds across Druggable Target Families
inferredcites →https://doi.org/10.1021/jm9602928openalex-snapshot
The Properties of Known Drugs. 1. Molecular Frameworks
inferredcites →https://doi.org/10.1021/jo8001276openalex-snapshot
Structural Diversity of Organic Chemistry. A Scaffold Analysis of the CAS Registry
inferredcites →https://doi.org/10.1021/ml900024vopenalex-snapshot
Exploring Target-Selectivity Patterns of Molecular Scaffolds
inferredcites →https://doi.org/10.1038/nbt0908-983openalex-snapshot
Data completeness—the Achilles heel of drug-target networks
inferredcites →https://doi.org/10.1038/nbt1228openalex-snapshot
Global mapping of pharmacological space
inferredcites →https://doi.org/10.1038/nbt1284openalex-snapshot
Relating protein pharmacology by ligand chemistry
inferredcites →https://doi.org/10.1038/nchembio.118openalex-snapshot
Network pharmacology: the next paradigm in drug discovery
inferredcites →https://doi.org/10.1038/nchembio.187openalex-snapshot
Interactive exploration of chemical space with Scaffold Hunter
inferredcites →https://doi.org/10.1038/nchembio.188openalex-snapshot
Bioactivity-guided mapping and navigation of chemical space
inferredcites →https://doi.org/10.1038/nchembio0807-442openalex-snapshot
Scaffold composition and biological relevance of screening libraries
inferredcites →https://doi.org/10.1038/nrd2220openalex-snapshot
A decade of fragment-based drug design: strategic advances and lessons learned
inferredcites →https://doi.org/10.1039/c0md00156bopenalex-snapshot
Global assessment of scaffold hopping potential for current pharmaceutical targets
inferredcites →https://doi.org/10.1073/pnas.0503647102openalex-snapshot
Charting biologically relevant chemical space: A structural classification of natural products (SCONP)
inferredcites →https://doi.org/10.1093/nar/gkl999openalex-snapshot
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1126/science.287.5460.1964openalex-snapshot
Target-Oriented and Diversity-Oriented Organic Synthesis in Drug Discovery
inferredcites →https://doi.org/10.2174/092986706775197999openalex-snapshot
Privileged Structures as Leads in Medicinal Chemistry
inferredcites →https://doi.org/10.2174/138955706778742768openalex-snapshot
On Scaffolds and Hopping in Medicinal Chemistry
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Chemoinformatic Characterization of the Chemical Space and Molecular Diversity of Compound Libraries
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EXPLORATION OF STRUCTURE–ACTIVITY RELATIONSHIPS (SARs) AND TRANSFER OF KEY ELEMENTS IN LEAD OPTIMIZATION
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CRITICAL ASSESSMENT OF VIRTUAL SCREENING FOR HIT IDENTIFICATION
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Tapentadol, a Clinically Proven Analgesic with Two Mechanisms
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Tapentadol – From Morphine and Tramadol to the Discovery of Tapentadol
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Scaffold Diversity in Medicinal Chemistry Space
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Cyclic Dipeptide: A Privileged Molecular Scaffold to Derive Structural Diversity and Functional Utility
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Activity Landscapes, Information Theory, and Structure – Activity Relationships
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Method for Systematic Assessment of Chemical Changes in Molecular Scaffolds with Conserved Topology and Application to the Analysis of Scaffold‐Activity Relationships
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PhIN: A Protein Pharmacology Interaction Network Database
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Some Aspects of 4H‐Pyrans Synthesis Based on 4‐Chloro‐1‐ethyl‐1H‐benzo[c][1,2]thiazine‐3‐carbaldehyde 2,2‐dioxide: Antimicrobial Activity of the Compounds Synthesized
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Molecular Scaffold Hopping via Holistic Molecular Representation
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Mapping Biological Activities to Different Types of Molecular Scaffolds: Exemplary Application to Protein Kinase Inhibitors
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PPAOT predictor: ARKA-RASTR strategy-driven rodent acute oral toxicity prediction for pyrazole and pyrrolidine scaffolds-based chemicals with intelligent mechanistic interpretation
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Systematic assessment of scaffold distances in ChEMBL: prioritization of compound data sets for scaffold hopping analysis in virtual screening
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Oxygen-containing fragments in natural products
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Is scaffold hopping a reliable indicator for the ability of computational methods to identify structurally diverse active compounds?
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Integrated machine learning and structural bioinformatics guided identification of novel molecular scaffolds as renin inhibitors
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Interpretable QSAR modelling for PPAR-γ agonist prediction by integrating a stacking strategy, docking, and MD simulations
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Scaffold Flatness: Reversing the Trend
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Analysis of Chemical Spaces: Implications for Drug Repurposing
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Synthesis and biological evaluation of novel dialkyl (4-amino-5H-chromeno[2,3-d]pyrimidin-5-yl)phosphonates
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Ethyl-4-(aryl)-6-methyl-2-(oxo/thio)-3,4-dihydro-1H-pyrimidine-5-carboxylates: Silica supported bismuth(III)triflate catalyzed synthesis and antioxidant activity
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Green synthesis of N-aryl-1-(2-bromo-4-methyl phenyl)-1H-tetrazol-5-amines as novel anti-cancer agents targeting tubulin-Combretastatin A4 complex and human non-small cell lung cancer cell lines
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Database of bioactive ring systems with calculated properties and its use in bioisosteric design and scaffold hopping
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Chemoinformatics: A view of the field and current trends in method development
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Systematic assessment of scaffold hopping versus activity cliff formation across bioactive compound classes following a molecular hierarchy
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Established and Emerging Trends in Computational Drug Discovery in the Structural Genomics Era
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Dataset of drugs, their molecular scaffolds and medical indications with interactive visualization
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Graph mining: procedure, application to drug discovery and recent advances
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Many drugs contain unique scaffolds with varying structural relationships to scaffolds of currently available bioactive compounds
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Machine learning and docking-based insights into descriptor, activity, and chirality cliffs of SYK inhibitors
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Beating pain with psychedelics: Matter over mind?
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Deep Learning-Based Ligand Design Using Shared Latent Implicit Fingerprints from Collaborative Filtering
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Magic Rings: Navigation in the Ring Chemical Space Guided by the Bioactive Rings
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An Open-Source Implementation of the Scaffold Identification and Naming System (SCINS) and Example Applications
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Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands
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Assessing the Growth of Bioactive Compounds and Scaffolds over Time: Implications for Lead Discovery and Scaffold Hopping
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Chemical Space Mapping and Structure–Activity Analysis of the ChEMBL Antiviral Compound Set
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Computational Exploration of Molecular Scaffolds in Medicinal Chemistry
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Recent Changes in the Scaffold Diversity of Organic Chemistry As Seen in the CAS Registry
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Structural Preferences and ADMET Regulation of Fluorinated Small-Molecule Drugs
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Green Synthesis, Antioxidant, and Plant Growth Regulatory Activities of Novel α-Furfuryl-2-alkylaminophosphonates
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Chemical Space Exploration of DprE1 Inhibitors Using Chemoinformatics and Artificial Intelligence
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XAI-ACSM: An Ensemble-Based Explainable Artificial Intelligence Framework for the Accurate Prediction of Anticancer Small Molecules
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Life Cycle Thinking in Early Drug Discovery: Reducing Environmental Impact and Animal Testing via Interpretable Machine Learning- and Chemometrics-Based Oral Acute Toxicity Screening
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Network Variants for Analyzing Target-Ligand Interactions
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Development of a Method To Consistently Quantify the Structural Distance between Scaffolds and To Assess Scaffold Hopping Potential
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Target Family-Directed Exploration of Scaffolds with Different SAR Profiles
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A Scaffold-Independent Subcellular Event-Based Analysis: Characterization of Significant Structural Modifications
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SAR Matrices: Automated Extraction of Information-Rich SAR Tables from Large Compound Data Sets
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Systematic Identification of Scaffolds Representing Compounds Active against Individual Targets and Single or Multiple Target Families
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Introducing the LASSO Graph for Compound Data Set Representation and Structure–Activity Relationship Analysis
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A conceptual framework for analysing and planning synthetic approaches to diverse lead-like scaffolds
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Structural enrichment of HTS compounds from available commercial libraries
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Systematic analysis of structural and activity relationships between conventional hierarchical and analog series-based scaffolds
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Bicyclic acetals: biological relevance, scaffold analysis, and applications in diversity-oriented synthesis
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Flow synthesis approaches to privileged scaffolds – recent routes reviewed for green and sustainable aspects
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Cheminformatics analysis of molecular datasets of transcription factors associated with quorum sensing in Pseudomonas aeruginosa
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Approaches for enhancing the analysis of chemical space for drug discovery
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Scopy: an integrated negative design python library for desirable HTS/VS database design
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RxnBLAST: molecular scaffold and reactive chemical environment feature extractor for biochemical reactions
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Toward an Efficient Approach to Identify Molecular Scaffolds Possessing Selective or Promiscuous Compounds
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Learning self-supervised molecular representations for drug–drug interaction prediction
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Bioactivity-explorer: a web application for interactive visualization and exploration of bioactivity data
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A general approach for retrosynthetic molecular core analysis
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Dataset’s chemical diversity limits the generalizability of machine learning predictions
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Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development
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“Molecular Anatomy”: a new multi-dimensional hierarchical scaffold analysis tool
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Scalable estimator of the diversity for de novo molecular generation resulting in a more robust QM dataset (OD9) and a more efficient molecular optimization
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Scaffold-based evaluation metrics for fair comparison of molecular generators
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Library Design, Chemical Space, and Drug Likeness
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- Library Design, Chemical Space, and Drug Likeness
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Rationalizing Structure and Target Relationships between Current Drugs
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Structural and Activity Profile Relationships Between Drug Scaffolds
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Cheminformatics techniques in antimalarial drug discovery and development from natural products 1: basic concepts
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Cheminformatics techniques in antimalarial drug discovery and development from natural products 2: Molecular scaffold and machine learning approaches
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Mechanistic and functional differentiation of tapentadol and tramadol
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Scalable Estimator of the Diversity for De Novo Molecular Generation Resulting in a More Robust QM Dataset (OD9) and a More Efficient Molecular Optimization.
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Cheminformatics analysis of molecular datasets of transcription factors associated with quorum sensing in Pseudomonas aeruginosa
inferred← citeshttps://doi.org/10.3389/fchem.2019.00510openalex-snapshot
Finding Constellations in Chemical Space Through Core Analysis
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Artificial intelligence and anti-cancer drugs: advancing discovery, personalization, and precision oncology
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Navigating the Chemical Space of ENR Inhibitors: A Comprehensive Analysis
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Biological Activity of Monoterpene-Based Scaffolds: A Natural Toolbox for Drug Discovery
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Synthesis of skeletally diverse alkaloid-like molecules: exploitation of metathesis substrates assembled from triplets of building blocks
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Virtual Compound Screening In Drug Discovery
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Structural Diversity and Potency Range Distribution of Scaffolds from Compounds Active Against Current Pharmaceutical Targets
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Analog Series-Based Scaffolds: Computational Design and Exploration of a New Type of Molecular Scaffolds for Medicinal Chemistry
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Computational Design of New Molecular Scaffolds for Medicinal Chemistry, Part II: Generalization of Analog Series-Based Scaffolds
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Collection of Analog Series-Based Scaffolds from Public Compound Sources
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Additional file 1 of “Molecular Anatomy”: a new multi-dimensional hierarchical scaffold analysis tool
inferred← citeshttps://doi.org/10.6084/m9.figshare.16726687openalex-snapshot
Additional file 1 of Scalable estimator of the diversity for de novo molecular generation resulting in a more robust QM dataset (OD9) and a more efficient molecular optimization
inferred← citeshttps://doi.org/10.6084/m9.figshare.26674736openalex-snapshot
Additional file 1 of Learning self-supervised molecular representations for drug–drug interaction prediction
inferred← citeshttps://doi.org/10.6084/m9.figshare.26674739openalex-snapshot
Additional file 2 of Learning self-supervised molecular representations for drug–drug interaction prediction
inferred← citeshttps://doi.org/10.6084/m9.figshare.26674742openalex-snapshot
Additional file 3 of Learning self-supervised molecular representations for drug–drug interaction prediction
inferred← citeshttps://doi.org/10.6084/m9.figshare.26674745openalex-snapshot
Additional file 4 of Learning self-supervised molecular representations for drug–drug interaction prediction
inferred← citeshttps://doi.org/10.6084/m9.figshare.26674748openalex-snapshot
Additional file 5 of Learning self-supervised molecular representations for drug–drug interaction prediction
inferred← citeshttps://doi.org/10.6084/m9.figshare.26674751openalex-snapshot
Additional file 6 of Learning self-supervised molecular representations for drug–drug interaction prediction
inferred← citeshttps://doi.org/10.6084/m9.figshare.26674754openalex-snapshot
Additional file 7 of Learning self-supervised molecular representations for drug–drug interaction prediction
inferred← citeshttps://doi.org/10.6084/m9.figshare.26674757openalex-snapshot
Additional file 8 of Learning self-supervised molecular representations for drug–drug interaction prediction
inferred← citeshttps://doi.org/10.70675/2b63c353z8184z4bbbzbfbcz9ce124edd263openalex-snapshot
New methods of multiscale chemical space analysis : visualization of structure-activity relationships and structural pattern extraction
inferred← citeshttps://doi.org/10.70675/5f1dee56z0ae7z4702zbd92z03596274e8f9openalex-snapshot
Computer-aided drug design of broad-spectrum antiviral compounds
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