ArticleJournal of medicinal chemistry2017
A Simple Representation of Three-Dimensional Molecular Structure.
Article in Journal of medicinal chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms.Chemical reviews · 2026Review
- Deep3D-DTA: A Tri-Modal Deep Learning Framework for Binding Affinity Prediction Leveraging 3D Structural Representations of Drugs and Targets.Interdisciplinary sciences, computational life sciences · 2026Article
- MutAIverse: an AI-powered, mechanism-backed platform for discovering novel DNA adducts and their precursor genotoxins.Journal of cheminformatics · 2026Article
- Multimodal deep-learning optimization of chiroptical properties in all-inorganic perovskite-coated TiONature communications · 2026Article
- A comprehensive review of cluster methods for drug-drug interaction network.Quantitative biology (Beijing, China) · 2026Review
- Neural Network Models for Prediction of Biological Activity using Molecular Dynamics Data: A Case of Photoswitchable Peptides.Molecular informatics · 2025Article
- Active Learning-Guided Hit Optimization for the Leucine-Rich Repeat Kinase 2 WDR Domain Based on In Silico Ligand-Binding Affinities.Journal of chemical information and modeling · 2025Article
- Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning.Journal of chemical theory and computation · 2025Article
- Clc-db: an open-source online database of chiral ligands and catalysts.Journal of cheminformatics · 2025Article
- A Fusion Deep Learning Model for Predicting Adverse Drug Reactions Based on Multiple Drug Characteristics.Life (Basel, Switzerland) · 2025Article
- Machine learning prediction of intestinal α-glucosidase inhibitors using a diverse set of ligands: a drug repurposing effort with drugBank database screening.In silico pharmacology · 2025Article
- Discovering geroprotectors through the explainable artificial intelligence-based platform AgeXtend.Nature aging · 2025Article
- NO classifier prediction of anti neuroinflammatory agents using text mining of 3D molecular fingerprints.Scientific reports · 2024Article
- A comprehensive comparison of deep learning-based compound-target interaction prediction models to unveil guiding design principles.Journal of cheminformatics · 2024Article
- SMTRI: A deep learning-based web service for predicting small molecules that target miRNA-mRNA interactions.Molecular therapy. Nucleic acids · 2024Article
- Article
- Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning forRSC medicinal chemistry · 2024Article
- Gram matrix: an efficient representation of molecular conformation and learning objective for molecular pretraining.Briefings in bioinformatics · 2024Article
- GPCR-IPL score: multilevel featurization of GPCR-ligand interaction patterns and prediction of ligand functions from selectivity to biased activation.Briefings in bioinformatics · 2024Article
- Repurposing Drugs for Inhibition against ALDH2 via a 2D/3D Ligand-Based Similarity Search and Molecular Simulation.Molecules (Basel, Switzerland) · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Statistical and machine learning approaches predict drug-to-target relationships from 2D small-molecule topology patterns. One might expect 3D information to improve these calculations. Here we apply the logic of the extended connectivity fingerprint (ECFP) to develop a rapid, alignment-invariant 3D representation of molecular conformers, the extended three-dimensional fingerprint (E3FP). By integrating E3FP with the similarity ensemble approach (SEA), we achieve higher precision-recall performance relative to SEA with ECFP on ChEMBL20 and equivalent receiver operating characteristic performance. We identify classes of molecules for which E3FP is a better predictor of similarity in bioactivity than is ECFP. Finally, we report novel drug-to-target binding predictions inaccessible by 2D fingerprints and confirm three of them experimentally with ligand efficiencies from 0.442-0.637 kcal/mol/heavy atom.
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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.