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Chemogenomics: Looking at biology through the lens of chemistry

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1 of the 83 references listed on this page is in the Retraction Watch database as retracted (export 2026-11-11): 10.1038/nm1491 (notice 2011-01-07).

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What this work says

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

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Analysis of multiblock and hierarchical PCA and PLS models

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Identification of Potent Ras Signaling Inhibitors by Pathway‐Selective Phenotype‐Based Screening

inferredcites →https://doi.org/10.1002/cmdc.200700026openalex-snapshot

Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off‐Target Effects from Chemical Structure

inferredcites →https://doi.org/10.1002/prot.20392openalex-snapshot

Linking tumor cell cytotoxicity to mechanism of drug action: An integrated analysis of gene expression, small‐molecule screening and structural databases

inferredcites →https://doi.org/10.1002/prot.20768openalex-snapshot

A chemogenomic analysis of the transmembrane binding cavity of human G‐protein‐coupled receptors

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Basic Local Alignment Search Tool

inferredcites →https://doi.org/10.1006/jmbi.1997.1525openalex-snapshot

Empirical statistical estimates for sequence similarity searches

inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot

Knowledge-based scoring function to predict protein-ligand interactions

inferredcites →https://doi.org/10.1007/s11095-007-9300-xopenalex-snapshot

Chemogenomic Analysis Identifies Geldanamycins as Substrates and Inhibitors of ABCB1

inferredcites →https://doi.org/10.1016/j.cbpa.2005.03.004openalex-snapshot

Assessment of structural diversity in combinatorial synthesis

inferredcites →https://doi.org/10.1016/j.chembiol.2003.08.010openalex-snapshot

Discovery of Inhibitors that Elucidate the Role of UCH-L1 Activity in the H1299 Lung Cancer Cell Line

inferredcites →https://doi.org/10.1016/j.compbiolchem.2004.09.003openalex-snapshot

Development of KiBank, a database supporting structure-based drug design

inferredcites →https://doi.org/10.1016/j.ddtec.2006.12.008openalex-snapshot

In silico target fishing: Predicting biological targets from chemical structure

inferredcites →https://doi.org/10.1016/j.entcs.2004.12.039openalex-snapshot

The Gaston Tool for Frequent Subgraph Mining

inferredcites →https://doi.org/10.1016/j.febslet.2008.02.024openalex-snapshot

Large‐scale prediction of drug–target relationships

inferredcites →https://doi.org/10.1016/j.jmgm.2005.09.013openalex-snapshot

Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials

inferredcites →https://doi.org/10.1016/j.jmgm.2007.02.005openalex-snapshot

Flexible 3D pharmacophores as descriptors of dynamic biological space

inferredcites →https://doi.org/10.1016/j.tips.2005.02.007openalex-snapshot

The efficiency of multi-target drugs: the network approach might help drug design

inferredcites →https://doi.org/10.1016/s0003-2697(03)00349-xopenalex-snapshot

High-throughput screening for the identification of small-molecule inhibitors of retinoblastoma protein phosphorylation in cells

inferredcites →https://doi.org/10.1016/s0022-2836(03)00428-5openalex-snapshot

Ligand Binding Energy and Catalytic Efficiency from Improved Packing within Receptors and Enzymes

inferredcites →https://doi.org/10.1016/s0304-4165(00)00187-2openalex-snapshot

Development of proteo-chemometrics: a novel technology for the analysis of drug-receptor interactions

inferredcites →https://doi.org/10.1016/s0960-894x(99)00577-6openalex-snapshot

Design and synthesis of highly potent fumagillin analogues from homology modeling for a human MetAP-2

inferredcites →https://doi.org/10.1016/s1074-5521(97)90198-8openalex-snapshot

Methionine aminopeptidase (type 2) is the common target for angiogenesis inhibitors AGM-1470 and ovalicin

inferredcites →https://doi.org/10.1016/s1367-5931(00)00229-5openalex-snapshot

Chemogenomic approaches to drug discovery

inferredcites →https://doi.org/10.1021/ci025531gopenalex-snapshot

Performance of Similarity Measures in 2D Fragment-Based Similarity Searching: Comparison of Structural Descriptors and Similarity Coefficients

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/ci049885eopenalex-snapshot

LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters

inferredcites →https://doi.org/10.1021/ci050006dopenalex-snapshot

Virtual Screen for Ligands of Orphan G Protein-Coupled Receptors

inferredcites →https://doi.org/10.1021/ci050065ropenalex-snapshot

Chemometric Analysis of Ligand Receptor Complementarity: Identifying Complementary Ligands Based on Receptor Information (CoLiBRI)

inferredcites →https://doi.org/10.1021/ci050221uopenalex-snapshot

An Automated System for the Analysis of G Protein-Coupled Receptor Transmembrane Binding Pockets: Alignment, Receptor-Based Pharmacophores, and Their Application

inferredcites →https://doi.org/10.1021/ci060003gopenalex-snapshot

Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases

inferredcites →https://doi.org/10.1021/ci0600509openalex-snapshot

SHED: Shannon Entropy Descriptors from Topological Feature Distributions

inferredcites →https://doi.org/10.1021/ci600197yopenalex-snapshot

“Bayes Affinity Fingerprints” Improve Retrieval Rates in Virtual Screening and Define Orthogonal Bioactivity Space: When Are Multitarget Drugs a Feasible Concept?

inferredcites →https://doi.org/10.1021/ci6002043openalex-snapshot

Parallel Screening: A Novel Concept in Pharmacophore Modeling and Virtual Screening

inferredcites →https://doi.org/10.1021/ci600300kopenalex-snapshot

Ligand-Based Approach to In Silico Pharmacology: Nuclear Receptor Profiling

inferredcites →https://doi.org/10.1021/ci8000259openalex-snapshot

Quantifying the Relationships among Drug Classes

inferredcites →https://doi.org/10.1021/ci8003896openalex-snapshot

Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner

inferredcites →https://doi.org/10.1021/ci9501047openalex-snapshot

Use of Structure−Activity Data To Compare Structure-Based Clustering Methods and Descriptors for Use in Compound Selection

inferredcites →https://doi.org/10.1021/jm00053a018openalex-snapshot

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds

inferredcites →https://doi.org/10.1021/jm00053a019openalex-snapshot

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds

inferredcites →https://doi.org/10.1021/jm000934yopenalex-snapshot

GRID/CPCA: A New Computational Tool To Design Selective Ligands

inferredcites →https://doi.org/10.1021/jm00125a025openalex-snapshot

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure

inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

inferredcites →https://doi.org/10.1021/jm0303195openalex-snapshot

Classification of Kinase Inhibitors Using a Bayesian Model

inferredcites →https://doi.org/10.1021/jm030520fopenalex-snapshot

Ligand-Based Structural Hypotheses for Virtual Screening

inferredcites →https://doi.org/10.1021/jm050363fopenalex-snapshot

Matrix Metalloproteinase Target Family Landscape: A Chemometrical Approach to Ligand Selectivity Based on Protein Binding Site Analysis

inferredcites →https://doi.org/10.1021/jm051139topenalex-snapshot

Robust Ligand-Based Modeling of the Biological Targets of Known Drugs

inferredcites →https://doi.org/10.1021/jm060902wopenalex-snapshot

Bridging Chemical and Biological Space: “Target Fishing” Using 2D and 3D Molecular Descriptors

inferredcites →https://doi.org/10.1021/jm980573aopenalex-snapshot

Identification of Novel Classes of Protein Kinase Inhibitors Using Combinatorial Peptide Chemistry Based on Functional Genomics Knowledge

inferredcites →https://doi.org/10.1023/a:1008781006867openalex-snapshot

Predicting binding modes, binding affinities and `hot spots' for protein-ligand complexes using a knowledge-based scoring function

inferredcites →https://doi.org/10.1038/3282openalex-snapshot

Drug target validation and identification of secondary drug target effects using DNA microarrays

inferredcites →https://doi.org/10.1038/35057062openalex-snapshot

Initial sequencing and analysis of the human genome

inferredcites →https://doi.org/10.1038/nature05981openalex-snapshot

Structure-based activity prediction for an enzyme of unknown function

inferredcites →https://doi.org/10.1038/nbt0908-983openalex-snapshot

Data completeness—the Achilles heel of drug-target networks

inferredcites →https://doi.org/10.1038/nbt1284openalex-snapshot

Relating protein pharmacology by ligand chemistry

inferredcites →https://doi.org/10.1038/nm1491openalex-snapshot

Genomic signatures to guide the use of chemotherapeutics

inferredcites →https://doi.org/10.1038/nrg1317openalex-snapshot

Chemogenomics: an emerging strategy for rapid target and drug discovery

inferredcites →https://doi.org/10.1038/sj.bjp.0707307openalex-snapshot

Chemogenomic approaches to rational drug design

inferredcites →https://doi.org/10.1039/b409813gopenalex-snapshot

Molecular similarity: a key technique in molecular informatics

inferredcites →https://doi.org/10.1039/b719372fopenalex-snapshot

Diversity-oriented synthesis; a spectrum of approaches and results

inferredcites →https://doi.org/10.1073/pnas.87.6.2264openalex-snapshot

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.

inferredcites →https://doi.org/10.1074/jbc.m006192200openalex-snapshot

Radicicol Binds and Inhibits Mammalian ATP Citrate Lyase

inferredcites →https://doi.org/10.1093/bioinformatics/bti703openalex-snapshot

Improved approach for proteochemometrics modeling: application to organic compound—amine G protein-coupled receptor interactions

inferredcites →https://doi.org/10.1093/bioinformatics/btn057openalex-snapshot

Tracing evolutionary pressure

inferredcites →https://doi.org/10.1093/nar/30.1.412openalex-snapshot

TTD: Therapeutic Target Database

inferredcites →https://doi.org/10.1093/nar/gkg103openalex-snapshot

GPCRDB information system for G protein-coupled receptors

inferredcites →https://doi.org/10.1093/nar/gkj067openalex-snapshot

DrugBank: a comprehensive resource for in silico drug discovery and exploration

inferredcites →https://doi.org/10.1093/nar/gkl1031openalex-snapshot

Database resources of the National Center for Biotechnology Information

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/10.1093/nar/gkm843openalex-snapshot

ChemBank: a small-molecule screening and cheminformatics resource database

inferredcites →https://doi.org/10.1093/nar/gkm862openalex-snapshot

SuperTarget and Matador: resources for exploring drug-target relationships

inferredcites →https://doi.org/10.1093/nar/gkm948openalex-snapshot

GLIDA: GPCR ligand database for chemical genomics drug discovery database and tools update

inferredcites →https://doi.org/10.1093/toxsci/kfl131openalex-snapshot

Chemical Genomic Profiling for Identifying Intracellular Targets of Toxicants Producing Parkinson's Disease

inferredcites →https://doi.org/10.1124/mol.104.002857openalex-snapshot

Proteochemometric Mapping of the Interaction of Organic Compounds with Melanocortin Receptor Subtypes

inferredcites →https://doi.org/10.1124/mol.64.2.382openalex-snapshot

Molecular Modes of Action of Artesunate in Tumor Cell Lines

inferredcites →https://doi.org/10.1126/science.1132939openalex-snapshot

The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease

inferredcites →https://doi.org/10.1177/107385840000600408openalex-snapshot

The Multiplicity of Serotonin Receptors: Uselessly Diverse Molecules or an Embarrassment of Riches?

inferredcites →https://doi.org/10.1177/1087057107306759openalex-snapshot

A Chemogenomic Analysis of the Human Proteome: Application to Enzyme Families

inferredcites →https://doi.org/10.1186/1471-2105-7-167openalex-snapshot

Prediction of indirect interactions in proteins

inferredcites →https://doi.org/10.1271/bbb.58.1579openalex-snapshot

Action of FR901228, a Novel Antitumor Bicyclic Depsipeptide Produced byChromo-bacterium violaceumNo. 968, on Ha-rasTransformed NIH3T3 Cells

inferredcites →https://doi.org/10.1358/dnp.2003.16.2.829326openalex-snapshot

Chemogenomics knowledge-based strategies in drug discovery

inferredcites →https://doi.org/10.1523/jneurosci.3364-04.2005openalex-snapshot

GABA Transporter Deficiency Causes Tremor, Ataxia, Nervousness, and Increased GABA-Induced Tonic Conductance in Cerebellum

inferredcites →https://doi.org/10.2174/138620707782507313openalex-snapshot

Chemogenomic Data Analysis: Prediction of Small-Molecule Targets and the Advent of Biological Fingerprints

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-3-319-09330-7_34openalex-snapshot

Predicting Potential Ligands for Orphan GPCRs Based on the Improved Laplacian Regularized Least Squares Method

inferred← citeshttps://doi.org/10.1016/j.csbj.2019.08.008openalex-snapshot

Current computational methods for predicting protein interactions of natural products

inferred← citeshttps://doi.org/10.1016/j.drudis.2011.05.005openalex-snapshot

A molecular informatics view on best practice in multi-parameter compound optimization

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00338openalex-snapshot

Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling

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/c4md00216dopenalex-snapshot

Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

inferred← citeshttps://doi.org/10.1186/1471-2105-11-316openalex-snapshot

A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization

inferred← citeshttps://doi.org/10.1186/1471-2105-13-s17-s11openalex-snapshot

Mapping small molecule binding data to structural domains

inferred← citeshttps://doi.org/10.1186/1758-2946-6-35openalex-snapshot

Proteochemometric modeling in a Bayesian framework

inferred← citeshttps://doi.org/10.70675/00fff70azab21z46edz8364z60031c95c00fopenalex-snapshot

Applications of proteochemometrics (PCM) : from species extrapolation to cell-line sensitivity modelling

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Characterizing protein domain associations by Small-molecule ligand binding

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