ArticleJournal of cheminformatics2021
DockStream: a docking wrapper to enhance de novo molecular design.
Article in Journal of cheminformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- DockM8: an all-in-one open-source platform for consensus virtual screening in drug design.Journal of cheminformatics · 2026Article
- SMILES2Docking: An Open-Source Desktop Workflow for Ligand Ionization, Stereochemistry-Aware Preparation and Semi-Empirical 3D Refinement.Molecular informatics · 2026Article
- EasyDock 1.3: An Automated Pipeline for Molecular Docking.Journal of chemical information and modeling · 2026Article
- Integrating machine learning-based molecular design with experimental validation for the discovery of EGFR inhibitors in lung cancer.Molecular diversity · 2026Article
- Assessing the factors influencing the quality of pocket-conditioned 3D generative models.Journal of cheminformatics · 2026Article
- CReM-pharm: de novo 3D pharmacophore-based design with synthetic accessibility awareness.Journal of cheminformatics · 2026Article
- AI accelerate the identification of druggable targets by 3D structures of proteins and compounds.NPJ precision oncology · 2026Review
- MolOrgGPT:Journal of chemical information and modeling · 2026Article
- An efficient computational chemistry approach to generating negative data for drug discovery pipeline validation.Frontiers in bioinformatics · 2026Article
- STELLA provides a drug design framework enabling extensive fragment-level chemical space exploration and balanced multi-parameter optimization.Scientific reports · 2025Article
- Identification of nanomolar adenosine ANature communications · 2025Article
- A Combination of Pharmacophore Generation, Ligand-based Virtual Screening, Atom-based 3D-QSAR, and Molecular Docking Studies on Febuxostat-based Amides Analogues as Anti-inflammatory Agents.Current drug discovery technologies · 2025Article
- Diverse Hits in De Novo Molecule Design: Diversity-Based Comparison of Goal-Directed Generators.Journal of chemical information and modeling · 2024Article
- Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning.JACS Au · 2024Article
- MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design.Journal of cheminformatics · 2024Article
- Sample efficient reinforcement learning with active learning for molecular design.Chemical science · 2024Article
- Reinvent 4: Modern AI-driven generative molecule design.Journal of cheminformatics · 2024Article
- DockOpt: A Tool for Automatic Optimization of Docking Models.Journal of chemical information and modeling · 2024Article
- On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data.Journal of cheminformatics · 2023Article
- EasyDock: customizable and scalable docking tool.Journal of cheminformatics · 2023Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently, we have released the de novo design platform REINVENT in version 2.0. This improved and extended iteration supports far more features and scoring function components, which allows bespoke and tailor-made protocols to maximize impact in small molecule drug discovery projects. A major obstacle of generative models is producing active compounds, in which predictive (QSAR) models have been applied to enrich target activity. However, QSAR models are inherently limited by their applicability domains. To overcome these limitations, we introduce a structure-based scoring component for REINVENT. DockStream is a flexible, stand-alone molecular docking wrapper that provides access to a collection of ligand embedders and docking backends. Using the benchmarking and analysis workflow provided in DockStream, execution and subsequent analysis of a variety of docking configurations can be automated. Docking algorithms vary greatly in performance depending on the target and the benchmarking and analysis workflow provides a streamlined solution to identifying productive docking configurations. We show that an informative docking configuration can inform the REINVENT agent to optimize towards improving docking scores using public data. With docking activated, REINVENT is able to retain key interactions in the binding site, discard molecules which do not fit the binding cavity, harness unused (sub-)pockets, and improve overall performance in the scaffold-hopping scenario. The code is freely available at https://github.com/MolecularAI/DockStream .
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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.