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How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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A Novel Chemogenomics Knowledge-Based Ligand Design Strategy—Application to G Protein-Coupled Receptors
inferredcites →https://doi.org/10.1002/9783527613083openalex-snapshot
Virtual Screening for Bioactive Molecules
inferredcites →https://doi.org/10.1002/9783527613106openalex-snapshot
Handbook of Molecular Descriptors
inferredcites →https://doi.org/10.1002/qsar.200530118openalex-snapshot
Comparison of Three Holographic Fingerprint Descriptors and their Binary Counterparts
inferredcites →https://doi.org/10.1002/qsar.200610091openalex-snapshot
Scaffold‐Hopping: How Far Can You Jump?
inferredcites →https://doi.org/10.1007/s10822-004-4067-1openalex-snapshot
Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments
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Kinomics—structural biology and chemogenomics of kinase inhibitors and targets
inferredcites →https://doi.org/10.1021/ci0001482openalex-snapshot
Selected Concepts and Investigations in Compound Classification, Molecular Descriptor Analysis, and Virtual Screening
inferredcites →https://doi.org/10.1021/ci010025xopenalex-snapshot
How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment
inferredcites →https://doi.org/10.1021/ci010132ropenalex-snapshot
Reoptimization of MDL Keys for Use in Drug Discovery
inferredcites →https://doi.org/10.1021/ci025569topenalex-snapshot
Similarity Metrics for Ligands Reflecting the Similarity of the Target Proteins
inferredcites →https://doi.org/10.1021/ci034207yopenalex-snapshot
Molecular Similarity Searching Using Atom Environments, Information-Based Feature Selection, and a Naïve Bayesian Classifier
inferredcites →https://doi.org/10.1021/ci034231bopenalex-snapshot
Comparison of Fingerprint-Based Methods for Virtual Screening Using Multiple Bioactive Reference Structures
inferredcites →https://doi.org/10.1021/ci0496144openalex-snapshot
Analysis of Data Fusion Methods in Virtual Screening: Similarity and Group Fusion
inferredcites →https://doi.org/10.1021/ci049615wopenalex-snapshot
Analysis of Data Fusion Methods in Virtual Screening: Theoretical Model
inferredcites →https://doi.org/10.1021/ci0498719openalex-snapshot
Similarity Searching of Chemical Databases Using Atom Environment Descriptors (MOLPRINT 2D): Evaluation of Performance
inferredcites →https://doi.org/10.1021/ci0500177openalex-snapshot
A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication
inferredcites →https://doi.org/10.1021/ci050296yopenalex-snapshot
The Use of Consensus Scoring in Ligand-Based Virtual Screening
inferredcites →https://doi.org/10.1021/ci060155bopenalex-snapshot
Novel 2D Fingerprints for Ligand-Based Virtual Screening
inferredcites →https://doi.org/10.1021/ci6004004openalex-snapshot
Clustering and Rule-Based Classifications of Chemical Structures Evaluated in the Biological Activity Space
inferredcites →https://doi.org/10.1021/ci6005504openalex-snapshot
Understanding False Positives in Reporter Gene Assays: in Silico Chemogenomics Approaches To Prioritize Cell-Based HTS Data
inferredcites →https://doi.org/10.1021/ci700099uopenalex-snapshot
Impact of Benchmark Data Set Topology on the Validation of Virtual Screening Methods: Exploration and Quantification by Spatial Statistics
inferredcites →https://doi.org/10.1021/ci9604605openalex-snapshot
Four Association Coefficients for Relating Molecular Similarity Measures
inferredcites →https://doi.org/10.1021/jm020155copenalex-snapshot
Do Structurally Similar Molecules Have Similar Biological Activity?
inferredcites →https://doi.org/10.1021/jm049654zopenalex-snapshot
A 3D Similarity Method for Scaffold Hopping from Known Drugs or Natural Ligands to New Chemotypes
inferredcites →https://doi.org/10.1021/jm050468iopenalex-snapshot
Scaffold Hopping through Virtual Screening Using 2D and 3D Similarity Descriptors: Ranking, Voting, and Consensus Scoring
inferredcites →https://doi.org/10.1021/jm960290nopenalex-snapshot
Neighborhood Behavior: A Useful Concept for Validation of “Molecular Diversity” Descriptors
inferredcites →https://doi.org/10.1021/jm9806998openalex-snapshot
New 4-Point Pharmacophore Method for Molecular Similarity and Diversity Applications: Overview of the Method and Applications, Including a Novel Approach to the Design of Combinatorial Libraries Containing Privileged Substructures
inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot
Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
inferredcites →https://doi.org/10.1023/a:1008752200506openalex-snapshot
Combination of molecular similarity measures using data fusion
inferredcites →https://doi.org/10.1023/b:jcam.0000017375.61558.adopenalex-snapshot
Comparison of correlation vector methods for ligand-based similarity searching
inferredcites →https://doi.org/10.1038/nbt1284openalex-snapshot
Relating protein pharmacology by ligand chemistry
inferredcites →https://doi.org/10.1039/b312875jopenalex-snapshot
Chemical genetics to chemical genomics: small molecules offer big insights
inferredcites →https://doi.org/10.1039/b409813gopenalex-snapshot
Molecular similarity: a key technique in molecular informatics
inferredcites →https://doi.org/10.1039/b409865jopenalex-snapshot
Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
inferredcites →https://doi.org/10.1080/10629369708039122openalex-snapshot
Characterization of Molecular Structures Using Topological Indices
inferredcites →https://doi.org/10.2174/138620707782507313openalex-snapshot
Chemogenomic Data Analysis: Prediction of Small-Molecule Targets and the Advent of Biological Fingerprints
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Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening
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Similarity Coefficients for Binary Chemoinformatics Data: Overview and Extended Comparison Using Simulated and Real Data Sets
inferred← citeshttps://doi.org/10.1021/ci300362xopenalex-snapshot
Scanning Structure–Activity Relationships with Structure–Activity Similarity and Related Maps: From Consensus Activity Cliffs to Selectivity Switches
inferred← citeshttps://doi.org/10.1021/ci3004094openalex-snapshot
Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints
inferred← citeshttps://doi.org/10.1021/ci300547gopenalex-snapshot
Combination of Similarity Rankings Using Data Fusion
inferred← citeshttps://doi.org/10.1021/ci3005868openalex-snapshot
Using Molecular Features of Xenobiotics to Predict Hepatic Gene Expression Response
inferred← citeshttps://doi.org/10.1021/ci300607ropenalex-snapshot
Bioturbo Similarity Searching: Combining Chemical and Biological Similarity To Discover Structurally Diverse Bioactive Molecules
inferred← citeshttps://doi.org/10.1021/ci400059popenalex-snapshot
Hit Expansion Approaches Using Multiple Similarity Methods and Virtualized Query Structures
inferred← citeshttps://doi.org/10.1021/ci400139jopenalex-snapshot
SimG: An Alignment Based Method for Evaluating the Similarity of Small Molecules and Binding Sites
inferred← citeshttps://doi.org/10.1021/ci400324uopenalex-snapshot
Noncontiguous Atom Matching Structural Similarity Function
inferred← citeshttps://doi.org/10.1021/ci400469uopenalex-snapshot
How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space
inferred← citeshttps://doi.org/10.1021/ci400620fopenalex-snapshot
Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method
inferred← citeshttps://doi.org/10.1021/ci500694copenalex-snapshot
Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT3A, Histamine H1, and Histamine H4Receptors
inferred← citeshttps://doi.org/10.1021/ci800379qopenalex-snapshot
Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs
inferred← citeshttps://doi.org/10.1021/ci900190zopenalex-snapshot
Alpha Shapes Applied to Molecular Shape Characterization Exhibit Novel Properties Compared to Established Shape Descriptors
inferred← citeshttps://doi.org/10.1021/ci900419kopenalex-snapshot
Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation
inferred← citeshttps://doi.org/10.1021/ci900498nopenalex-snapshot
HPPD: Ligand- and Target-Based Virtual Screening on a Herbicide Target
inferred← citeshttps://doi.org/10.1021/jm300280eopenalex-snapshot
A Prospective Cross-Screening Study on G-Protein-Coupled Receptors: Lessons Learned in Virtual Compound Library Design
inferred← citeshttps://doi.org/10.1021/jm3003069openalex-snapshot
Identifying Novel Adenosine Receptor Ligands by Simultaneous Proteochemometric Modeling of Rat and Human Bioactivity Data
inferred← citeshttps://doi.org/10.1021/jm3013486openalex-snapshot
Identification and Characterization of New DNA G-Quadruplex Binders Selected by a Combination of Ligand and Structure-Based Virtual Screening Approaches
inferred← citeshttps://doi.org/10.1021/jm4011302openalex-snapshot
Discovery of Novel Small-Molecule Inhibitors of BRD4 Using Structure-Based Virtual Screening
inferred← citeshttps://doi.org/10.1021/mp300237zopenalex-snapshot
Molecular Fingerprint-Based Artificial Neural Networks QSAR for Ligand Biological Activity Predictions
inferred← citeshttps://doi.org/10.1021/tx4000182openalex-snapshot
Carcinogenicity Prediction of Noncongeneric Chemicals by a Support Vector Machine
inferred← citeshttps://doi.org/10.1038/s41598-019-40640-4openalex-snapshot
Use of machine learning to identify novel, behaviorally active antagonists of the insect odorant receptor co-receptor (Orco) subunit
inferred← citeshttps://doi.org/10.1038/s41598-022-22992-6openalex-snapshot
The use of machine learning modeling, virtual screening, molecular docking, and molecular dynamics simulations to identify potential VEGFR2 kinase inhibitors
inferred← citeshttps://doi.org/10.1038/s42003-022-03763-5openalex-snapshot
Integrating cell morphology with gene expression and chemical structure to aid mitochondrial toxicity detection
inferred← citeshttps://doi.org/10.1039/9781788018982-00231openalex-snapshot
Machine Learning in Drug Design
inferred← citeshttps://doi.org/10.1039/c0md00165aopenalex-snapshot
Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets
inferred← citeshttps://doi.org/10.1039/c9me00109copenalex-snapshot
Less may be more: an informed reflection on molecular descriptors for drug design and discovery
inferred← citeshttps://doi.org/10.1055/s-0034-1396314openalex-snapshot
How to Valorize Biodiversity? Letʼs Go Hashing, Extracting, Filtering, Mining, Fishing
inferred← citeshttps://doi.org/10.1063/5.0156222openalex-snapshot
Combining machine learning and molecular simulations to predict the stability of amorphous drugs
inferred← citeshttps://doi.org/10.1073/pnas.1015024108openalex-snapshot
Quantifying structure and performance diversity for sets of small molecules comprising small-molecule screening collections
inferred← citeshttps://doi.org/10.1080/07391102.2023.2275176openalex-snapshot
Exploring the potential of machine learning to design antidiabetic molecules: a comprehensive study with experimental validation
inferred← citeshttps://doi.org/10.1080/10408444.2024.2386260openalex-snapshot
Molecular similarity in chemical informatics and predictive toxicity modeling: from quantitative read-across (q-RA) to quantitative read-across structure–activity relationship (q-RASAR) with the application of machine learning
inferred← citeshttps://doi.org/10.1080/17460441.2018.1465926openalex-snapshot
Progress with modeling activity landscapes in drug discovery
inferred← citeshttps://doi.org/10.1080/17460441.2021.1901685openalex-snapshot
The challenges of generalizability in artificial intelligence for ADME/Tox endpoint and activity prediction
inferred← citeshttps://doi.org/10.1093/bib/bbab291openalex-snapshot
Comparative analysis of molecular fingerprints in prediction of drug combination effects
inferred← citeshttps://doi.org/10.1093/bib/bbaf635openalex-snapshot
Computational approaches to enzymatic reaction assignment: a review of methods, validations, and future directions
inferred← citeshttps://doi.org/10.1093/bib/bby061openalex-snapshot
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
inferred← citeshttps://doi.org/10.1093/bib/bby069openalex-snapshot
Review and comparative assessment of similarity-based methods for prediction of drug–protein interactions in the druggable human proteome
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv529openalex-snapshot
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel
inferred← citeshttps://doi.org/10.1093/nar/gkq325openalex-snapshot
Frog2: Efficient 3D conformation ensemble generator for small compounds
inferred← citeshttps://doi.org/10.1093/nar/gku1212openalex-snapshot
CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering
inferred← citeshttps://doi.org/10.1093/toxsci/kfaf067openalex-snapshot
Identifying environmental chemicals impacting neurodevelopment using a random mixture-based screening approach
inferred← citeshttps://doi.org/10.1101/2021.04.16.439299openalex-snapshot
Comparative analysis of molecular representations in prediction of drug combination effects
inferred← citeshttps://doi.org/10.1101/2024.03.25.586580openalex-snapshot
Bridging polarities in metabolomics: Cross-ionization mode chemical similarity prediction between tandem mass spectra
inferred← citeshttps://doi.org/10.1101/2025.06.16.659994openalex-snapshot
Count your bits: fingerprint benchmarking to assess broad chemical space representation
inferred← citeshttps://doi.org/10.1109/access.2020.3046190openalex-snapshot
Benchmarking Small-Dataset Structure-Activity-Relationship Models for Prediction of Wnt Signaling Inhibition
inferred← citeshttps://doi.org/10.1109/bibm.2016.7822693openalex-snapshot
Benchmarking platform for ligand-based virtual screening
inferred← citeshttps://doi.org/10.1109/bibm47256.2019.8983077openalex-snapshot
Chemical Similarity Based on Map Edit Distance
inferred← citeshttps://doi.org/10.1109/bibm47256.2019.8983340openalex-snapshot
TOP: Towards Better Toxicity Prediction by Deep Molecular Representation Learning
inferred← citeshttps://doi.org/10.1109/gcat52182.2021.9587658openalex-snapshot
Ensemble Machine Learning Approaches in Molecular Fingerprint based Virtual screening
inferred← citeshttps://doi.org/10.1109/ic3ecsbhi63591.2025.10990995openalex-snapshot
A Computational Outlook on the Potential of Cyanobacteria in Cancer Treatment and Drug Discovery
inferred← citeshttps://doi.org/10.1109/icde60146.2024.00093openalex-snapshot
DROPP: Structure-Aware PCA for Ordered Data: A General Method and its Applications in Climate Research and Molecular Dynamics
inferred← citeshttps://doi.org/10.1109/icdmw.2016.0044openalex-snapshot
Ligand-Based Virtual Screening with Co-regularised Support Vector Regression
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2009.00930.xopenalex-snapshot
Reduction and Recombination of Fingerprints of Different Design Increase Compound Recall and the Structural Diversity of Hits
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2011.01100.xopenalex-snapshot
Increased Diversity of Libraries from Libraries: Chemoinformatic Analysis of Bis‐Diazacyclic Libraries
inferred← citeshttps://doi.org/10.1111/jtxs.12248openalex-snapshot
Classification of starch gel texture for the elderly diets based on instrumental and sensory methodology
inferred← citeshttps://doi.org/10.1145/2184512.2184528openalex-snapshot
Improving molecular fingerprint similarity via enhanced folding
inferred← citeshttps://doi.org/10.1146/annurev-pharmtox-011112-140248openalex-snapshot
Systems Pharmacology to Predict Drug Toxicity: Integration Across Levels of Biological Organization
inferred← citeshttps://doi.org/10.1177/0165551512470042openalex-snapshot
Comparison of chemical similarity measures using different numbers of query structures
inferred← citeshttps://doi.org/10.1177/1087057113501390openalex-snapshot
Benchmarking of Multivariate Similarity Measures for High-Content Screening Fingerprints in Phenotypic Drug Discovery
inferred← citeshttps://doi.org/10.1177/1087057114522515openalex-snapshot
Small-Molecule Library Subset Screening as an Aid for Accelerating Lead Identification
inferred← citeshttps://doi.org/10.1186/1472-6769-9-6openalex-snapshot
DG-AMMOS: A New tool to generate 3D conformation of small molecules using D istance G eometry and A utomated M olecular M echanics O ptimization for in silico S creening
inferred← citeshttps://doi.org/10.1186/1752-153x-4-s1-s4openalex-snapshot
CAESAR models for developmental toxicity
inferred← citeshttps://doi.org/10.1186/1756-0381-6-7openalex-snapshot
Optimization and visualization of the edge weights in optimal assignment methods for virtual screening
inferred← citeshttps://doi.org/10.1186/1758-2946-1-14openalex-snapshot
Optimal assignment methods for ligand-based virtual screening
inferred← citeshttps://doi.org/10.1186/1758-2946-3-23openalex-snapshot
4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening
inferred← citeshttps://doi.org/10.1186/1758-2946-4-28openalex-snapshot
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis
inferred← citeshttps://doi.org/10.1186/1758-2946-5-26openalex-snapshot
Open-source platform to benchmark fingerprints for ligand-based virtual screening
inferred← citeshttps://doi.org/10.1186/1758-2946-5-41openalex-snapshot
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets
inferred← citeshttps://doi.org/10.1186/1758-2946-5-42openalex-snapshot
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets
inferred← citeshttps://doi.org/10.1186/1758-2946-5-49openalex-snapshot
Are phylogenetic trees suitable for chemogenomics analyses of bioactivity data sets: the importance of shared active compounds and choosing a suitable data embedding method, as exemplified on Kinases
inferred← citeshttps://doi.org/10.1186/1758-2946-6-23openalex-snapshot
A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening
inferred← citeshttps://doi.org/10.1186/1758-2946-6-35openalex-snapshot
Proteochemometric modeling in a Bayesian framework
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