ArticleCell chemical biology2019
Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries.
Article in Cell chemical biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
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Who cites it
34 citing papers in PubMed.
- Big Data and Artificial Intelligence in Cancer Drug Discovery: Promise, Challenges, and Emerging Opportunities.Cancers · 2026Review
- A human iPSC-derived sensory neuron platform for high-throughput discovery of neuroprotectants against chemotherapy-induced peripheral neuropathy.Cell reports. Medicine · 2026Article
- Polypharmacology is an enduring and nearly universal property of kinase inhibitors.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data.Molecular & cellular proteomics : MCP · 2025Article
- Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery.Genome medicine · 2025Article
- ChemoDOTS: a web server to design chemistry-driven focused libraries.Nucleic acids research · 2024Article
- Meta-learning-based Inductive logistic matrix completion for prediction of kinase inhibitors.Journal of cheminformatics · 2024Article
- Repurposing lansoprazole to alleviate metabolic syndromeActa pharmaceutica Sinica. B · 2024Article
- Illuminating function of the understudied druggable kinome.Drug discovery today · 2024Review
- Identification of Collagen-Suppressive Agents in Keloidal Fibroblasts Using a High-Content, Phenotype-Based Drug Screen.JID innovations : skin science from molecules to population health · 2024Article
- A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.Journal of chemical information and modeling · 2023Article
- Chemogenomic library design strategies for precision oncology, applied to phenotypic profiling of glioblastoma patient cells.iScience · 2023Article
- Artificial Intelligence Assisted Pharmacophore Design for Philadelphia Chromosome-Positive Leukemia with Gamma-Tocotrienol: A Toxicity Comparison Approach with Asciminib.Biomedicines · 2023Article
- Pharmacological approaches to understanding protein kinase signaling networks.Frontiers in pharmacology · 2023Review
- Identification of Aloe-derived natural products as prospective lead scaffolds for SARS-CoV-2 main protease (MBioorganic & medicinal chemistry letters · 2022Article
- Expanding the search for small-molecule antibacterials by multidimensional profiling.Nature chemical biology · 2022Review
- Whole blood transcriptomic profiling identifies molecular pathways related to cardiovascular mortality in heart failure.European journal of heart failure · 2022Article
- Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs.PLoS computational biology · 2022Article
- Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.Genome research · 2022Article
- A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease.eLife · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Libraries of well-annotated small molecules have many uses in chemical genetics, drug discovery, and therapeutic repurposing. Multiple libraries are available, but few data-driven approaches exist to compare them and design new libraries. We describe an approach to scoring and creating libraries based on binding selectivity, target coverage, and induced cellular phenotypes as well as chemical structure, stage of clinical development, and user preference. The approach, available via the online tool http://www.smallmoleculesuite.org, assembles sets of compounds with the lowest possible off-target overlap. Analysis of six kinase inhibitor libraries using our approach reveals dramatic differences among them and led us to design a new LSP-OptimalKinase library that outperforms existing collections in target coverage and compact size. We also describe a mechanism of action library that optimally covers 1,852 targets in the liganded genome. Our tools facilitate creation, analysis, and updates of both private and public compound collections.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.