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Investigation of the Use of Spectral Clustering for the Analysis of Molecular Data

https://doi.org/10.1021/ci500480b
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What this work says

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

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Reviews in Computational Chemistry
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Clustering Methods and Their Uses in Computational Chemistry
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Quantitative Measures of Change Based on Feature Organization: Eigenvalues and Eigenvectors
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SCOP: A structural classification of proteins database for the investigation of sequences and structures
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Introduction to Linear Algebra
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An Introduction To Chemoinformatics
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An improved algorithm for hierarchical clustering using strong components
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Accuracy and effectiveness of the Lanczos algorithm for the symmetric eigenproblem
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Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
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Early phase drug discovery: Cheminformatics and computational techniques in identifying lead series
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Discovery of novel inhibitors of Trypanosoma cruzi trans-sialidase from in silico screening
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Chemical diversity and biological activity
inferredcites →https://doi.org/10.1016/j.drudis.2009.05.011openalex-snapshot
Picking up the pieces with FBDD or FADD: invest early for future success
inferredcites →https://doi.org/10.1016/j.jmb.2010.10.015openalex-snapshot
Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms
inferredcites →https://doi.org/10.1016/j.jmgm.2009.06.006openalex-snapshot
Clustering files of chemical structures using the Székely–Rizzo generalization of Ward's method
inferredcites →https://doi.org/10.1021/bk-2005-0894.ch011openalex-snapshot
Clustering Compound Data: Asymmetric Clustering of Chemical Datasets
inferredcites →https://doi.org/10.1021/ci010132ropenalex-snapshot
Reoptimization of MDL Keys for Use in Drug Discovery
inferredcites →https://doi.org/10.1021/ci034001xopenalex-snapshot
Analysis and Display of the Size Dependence of Chemical Similarity Coefficients
inferredcites →https://doi.org/10.1021/ci100050topenalex-snapshot
Extended-Connectivity Fingerprints
inferredcites →https://doi.org/10.1021/ci4000882openalex-snapshot
Fighting Obesity with a Sugar-Based Library: Discovery of Novel MCH-1R Antagonists by a New Computational–VAST Approach for Exploration of GPCR Binding Sites
inferredcites →https://doi.org/10.1021/ci400106gopenalex-snapshot
Do Not Hesitate to Use Tversky—and Other Hints for Successful Active Analogue Searches with Feature Count Descriptors
inferredcites →https://doi.org/10.1021/ci600565ropenalex-snapshot
Development of a Spectral Clustering Method for the Analysis of Molecular Data Sets
inferredcites →https://doi.org/10.1021/ci980109eopenalex-snapshot
Molecular Diversity and Representativity in Chemical Databases
inferredcites →https://doi.org/10.1021/jm8000373openalex-snapshot
Recent Developments in Fragment-Based Drug Discovery
inferredcites →https://doi.org/10.1039/b409865jopenalex-snapshot
Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
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Numerical Recipes: The Art of Scientific Computing
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Hierarchical Grouping to Optimize an Objective Function
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3D Pharmacophore, hierarchical methods, and 5-HT4receptor binding data
inferredcites →https://doi.org/10.1093/nar/gkj515openalex-snapshot
Spectral clustering of protein sequences
inferredcites →https://doi.org/10.1093/nar/gkr777openalex-snapshot
ChEMBL: a large-scale bioactivity database for drug discovery
inferredcites →https://doi.org/10.1093/protein/9.11.1063openalex-snapshot
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
inferredcites →https://doi.org/10.1109/34.868688openalex-snapshot
Normalized cuts and image segmentation
inferredcites →https://doi.org/10.1109/cvpr.1996.517115openalex-snapshot
Quantitative measures of change based on feature organization: eigenvalues and eigenvectors
inferredcites →https://doi.org/10.1109/tcbb.2012.108openalex-snapshot
SC³: Triple Spectral Clustering-Based Consensus Clustering Framework for Class Discovery from Cancer Gene Expression Profiles
inferredcites →https://doi.org/10.1137/1.9781611971163openalex-snapshot
The Symmetric Eigenvalue Problem
inferredcites →https://doi.org/10.1186/1471-2105-11-120openalex-snapshot
SCPS: a fast implementation of a spectral method for detecting protein families on a genome-wide scale
inferredcites →https://doi.org/10.1186/1758-2946-4-29openalex-snapshot
Fast rule-based bioactivity prediction using associative classification mining
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Handbook of Parallel Computing and Statistics
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Clustering Algorithms.
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Effectiveness of 2D Fingerprints for Scaffold Hopping
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Matrix Computations
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An iteration method for the solution of the eigenvalue problem of linear differential and integral operators
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Advances in Neural Information Processing Systems 14

What points at this work

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

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Optimal Selection of Bands for Hyperspectral Images Using Spectral Clustering
inferred← citeshttps://doi.org/10.1007/s41870-024-01815-zopenalex-snapshot
Privacy-preserving eigenvector computation with applications in spectral clustering
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Ecological risk assessment and source apportionment of potentially toxic elements in an emerging mining zone region of northwestern Ghana
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00420openalex-snapshot
Nested TMAPs to Visualize Billions of Molecules
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00689openalex-snapshot
Development of New Methods Needs Proper Evaluation—Benchmarking Sets for Machine Learning Experiments for Class A GPCRs
inferred← citeshttps://doi.org/10.1039/d5dd00030kopenalex-snapshot
BitBIRCH: efficient clustering of large molecular libraries
inferred← citeshttps://doi.org/10.1101/2024.08.10.607459openalex-snapshot
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inferred← citeshttps://doi.org/10.1109/cisat71030.2026.11682430openalex-snapshot
Identification of Molecular Subtypes and Prognostic Analysis of Gastric Cancer Based on Adaptive LASSO Dimension Reduction and Spectral Clustering
inferred← citeshttps://doi.org/10.1145/3556677.3556684openalex-snapshot
Comparison of cancer classification algorithms based on clustering analysis
inferred← citeshttps://doi.org/10.1155/2015/916240openalex-snapshot
Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments
inferred← citeshttps://doi.org/10.1186/s12859-025-06278-yopenalex-snapshot
SMILES alignment: a dynamic programming approach for the alignment of metabolites and other small organic molecules
inferred← citeshttps://doi.org/10.1186/s13321-017-0198-yopenalex-snapshot
Analysis of drug–endogenous human metabolite similarities in terms of their maximum common substructures
inferred← citeshttps://doi.org/10.1186/s40537-025-01231-5openalex-snapshot
A novel approach to automating unsupervised estimation of class distribution
inferred← citeshttps://doi.org/10.3389/fphar.2016.00266openalex-snapshot
MetMaxStruct: A Tversky-Similarity-Based Strategy for Analysing the (Sub)Structural Similarities of Drugs and Endogenous Metabolites
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