ArticleChemical science2019
Scaffold-based molecular design with a graph generative model.
Article in Chemical science, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- MMP2Mol: a matched molecular pairs-based framework for ligand-based de novo drug design.Briefings in bioinformatics · 2026Article
- EvoDiffMol: evolutionary diffusion framework for 3D molecular design with optimized properties.Journal of cheminformatics · 2026Article
- Deep learning for small-molecule drug discovery: From molecular design to clinical translation.Journal of pharmaceutical analysis · 2026Review
- Modular Framework for 3D Molecular Generation in Computational Chemistry Applications.Journal of the American Chemical Society · 2026Article
- AI in Drug Discovery: Clinical Failures, Regulatory Reality, and the Validation Crisis Behind the Hype.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Generative pretraining for drug molecule design with bidirectional structure-property optimization.Communications chemistry · 2026Article
- Design and optimization of novel succinate dehydrogenase inhibitors against agricultural fungi based on transformer model.Molecular diversity · 2026Article
- An effective fragment-based dual conditional diffusion framework for molecular generation.Briefings in bioinformatics · 2026Article
- Molecule generation for drug design: A graph learning perspective.Fundamental research · 2026Review
- Integrating artificial intelligence across the cancer drug discovery pipeline using a design-test-refine workflow.Frontiers in oncology · 2026Review
- Bidirectional reinforcement learning neural network for constrained molecular design.Scientific reports · 2025Article
- Structure-based design of anticancer drugs based on β-elemene: Research foundations and development potential.Journal of pharmaceutical analysis · 2025Review
- Multitarget Generate Electrolyte Additive for Lithium Metal Batteries.Advanced materials (Deerfield Beach, Fla.) · 2025Article
- Bridging chemical space and biological efficacy: advances and challenges in applying generative models in structural modification of natural products.Natural products and bioprospecting · 2025Review
- CardioGenAI: a machine learning-based framework for re-engineering drugs for reduced hERG liability.Journal of cheminformatics · 2025Article
- Generative Deep Learning-Based Efficient Design of Organic Molecules with Tailored Properties.ACS central science · 2025Article
- Evaluation of reinforcement learning in transformer-based molecular design.Journal of cheminformatics · 2024Article
- Stereoselective Access to Diverse Alkaloid-Like Scaffolds via an Oxidation/Double-Mannich Reaction Sequence.Organic letters · 2024Article
- Equivariant score-based generative diffusion framework for 3D molecules.BMC bioinformatics · 2024Article
- NIMO: A Natural Product-Inspired Molecular Generative Model Based on Conditional Transformer.Molecules (Basel, Switzerland) · 2024Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Searching for new molecules in areas like drug discovery often starts from the core structures of known molecules. Such a method has called for a strategy of designing derivative compounds retaining a particular scaffold as a substructure. On this account, our present work proposes a graph generative model that targets its use in scaffold-based molecular design. Our model accepts a molecular scaffold as input and extends it by sequentially adding atoms and bonds. The generated molecules are then guaranteed to contain the scaffold with certainty, and their properties can be controlled by conditioning the generation process on desired properties. The learned rule of extending molecules can well generalize to arbitrary kinds of scaffolds, including those unseen during learning. In the conditional generation of molecules, our model can simultaneously control multiple chemical properties despite the search space constrained by fixing the substructure. As a demonstration, we applied our model to designing inhibitors of the epidermal growth factor receptor and show that our model can employ a simple semi-supervised extension to broaden its applicability to situations where only a small amount of data is available.
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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.