ArticleJournal of cheminformatics2025
GNINA 1.3: the next increment in molecular docking with deep learning.
Article in Journal of cheminformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
82 citing papers in PubMed.
- A critical appraisal of structure-based virtual screening, binding free energy methods, and AI-driven molecular design across the evolving computational landscape of drug discovery.Journal of computer-aided molecular design · 2026Review
- Target discovery and drug design in the era of artificial intelligence.Medicinal chemistry research : an international journal for rapid communications on design and mechanisms of action of biologically active agents · 2026Review
- Molecularly diverse lonazolac-inspired pyrazole-cyanopyridin-2-one conjugates: design, synthesis, in vitro, in vivo and in silico studies as multi-target anti-inflammatory agents.Molecular diversity · 2026Article
- Overcoming Docetaxel Resistance in Prostate Cancer by Targeting Cell Cycle Progression with Narciclasine-Based Compounds.ACS omega · 2026Article
- Robots and Minimal, Physics-Informed Features: A Hybrid Framework for Enzyme Catalysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Enhanced Line Search Improves Robustness and Efficiency of Pose Sampling in Protein-Ligand Docking.Journal of chemical theory and computation · 2026Article
- Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design.Nucleic acids research · 2026Article
- Design, Synthesis, and Biological Evaluation of Anthracene Derivatives as Potent Antioxidants: Experimental, DFT, and Docking Studies.Chemical biology & drug design · 2026Article
- The nematode Caenorhabditis elegans has a cationic amphiphilic drug (CAD) defense system.PLoS biology · 2026Article
- The Different Faces of the Selective Human Telomerase Inhibitor: BIBR1532 and Its Derivatives.Current issues in molecular biology · 2026Article
- PARP3 Promotes SARS-CoV-2 Replication via Interaction with the Viral Nucleocapsid Protein.The Kobe journal of medical sciences · 2026Article
- Evaluating molecular docking for binding affinity predictions: a systematic analysis of key parameters and the utility of AlphaFold2 structures for the Schrödinger dataset.Journal of computer-aided molecular design · 2026Article
- 5-Nitrothiazol-Clofibric Acid Analogs as Potent Agents Against Nitazoxanide-ResistantMolecules (Basel, Switzerland) · 2026Article
- Beyond the Score: Fixed-Budget Benchmarking of Virtual Screening Integration Strategies for Decision-Centric Drug Discovery.International journal of molecular sciences · 2026Article
- Combining Triazole Scaffold Repurposing and Generative Transformer Architecture for Structure-Based Inhibitor Design Targeting the LasR Quorum Sensing Receptor ofPharmaceuticals (Basel, Switzerland) · 2026Article
- EasyDock 1.3: An Automated Pipeline for Molecular Docking.Journal of chemical information and modeling · 2026Article
- Computational Investigation of Cinnamon Phytochemicals Targeting Key Cancer Signaling Pathways: Molecular Docking, ADMET and Molecular Dynamics Simulations Analysis.Current issues in molecular biology · 2026Article
- MOZAIC: compound growth via in silico reactions and global optimization using Conformational Space Annealing.Bioinformatics (Oxford, England) · 2026Article
- Identification of Repurposed Drugs Against Monkeypox Virus Through Comprehensive Virtual Screening.Biotechnology journal · 2026Article
- Seaweeds From the Veracruz Rocky Shore (Mexico) as Novel Sources of Bioactive Compounds Against Fusarium Species Pathogenic to Corn (Zea mays).Chemistry & biodiversity · 2026Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Computer-aided drug design has the potential to significantly reduce the astronomical costs of drug development, and molecular docking plays a prominent role in this process. Molecular docking is an in silico technique that predicts the bound 3D conformations of two molecules, a necessary step for other structure-based methods. Here, we describe version 1.3 of the open-source molecular docking software GNINA. This release updates the underlying deep learning framework to PyTorch, resulting in more computationally efficient docking and paving the way for seamless integration of other deep learning methods into the docking pipeline. We retrained our CNN scoring functions on the updated CrossDocked2020 v1.3 dataset and introduce knowledge-distilled CNN scoring functions to facilitate high-throughput virtual screening with GNINA. Furthermore, we add functionality for covalent docking, where an atom of the ligand is covalently bound to an atom of the receptor. This update expands the scope of docking with GNINA and further positions GNINA as a user-friendly, open-source molecular docking framework. GNINA is available at https://github.com/gnina/gnina .Scientific contributions: GNINA 1.3 is an open source a molecular docking tool with enhanced support for covalent docking and updated deep learning models for more effective docking and screening.
Indexed as
Identifiers
What OpenQuestion holds
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.