ArticleJournal of chemical information and modeling2025
Meeko: Molecule Parametrization and Software Interoperability for Docking and Beyond.
Article in Journal of chemical information and modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed.
- Integrated Experimental, Chemometric, and In Silico Analyses of Larvicidal Supercritical Extracts From Myrtaceae Species Against Aedes aegypti.Chemistry & biodiversity · 2026Article
- PockLigGPT: Pocket-Sequence-Conditioned Molecular Generation with GPTs and RL.Journal of chemical information and modeling · 2026Article
- Enhanced Line Search Improves Robustness and Efficiency of Pose Sampling in Protein-Ligand Docking.Journal of chemical theory and computation · 2026Article
- Biopesticidal Potential of theInternational journal of molecular sciences · 2026Article
- An extension of jamdock-suite for virtual screening from raw chemical datasets.STAR protocols · 2026Article
- OXR1 is a dual redox-mitochondrial checkpoint governing osteoclast differentiation and bone loss in an osteoporosis mouse model.Nature communications · 2026Article
- Bend and Snap: Computationally Exploring the Helix Bias for Classifying Abl Kinase Allosteric Modulators.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
- From Descriptor Learning to Binding Stability: An Explainable Machine Learning Pipeline for EGFR Double-Mutant Inhibitor Discovery.International journal of molecular sciences · 2026Article
- A Length-Aware C-Terminal Rule for Prioritizing Short ACE-Inhibitory Peptides from Food Protein Hydrolysates.Foods (Basel, Switzerland) · 2026Article
- QSAR-Guided Virtual Screening and Molecular Dynamics Reveal Olaparib as a Repurposing Lead Against α-Synuclein Aggregation.International journal of molecular sciences · 2026Article
- Ameliorative Effects of a Naphthoquinone Derivative With β-Amyloid Aggregation Inhibitory Activity on Cognitive Impairment and Metabolite Analysis of the Blood and Brains of Mice.Drug development research · 2026Article
- A synergistic deep learning and machine learning framework for screening heterocyclic compounds against ALDH1A1.Molecular diversity · 2026Article
- FDA-Approved Drug Repurposing as p53 Mutants Rescue Candidates Using Structure-Based Virtual Screening and Molecular Simulations.International journal of molecular sciences · 2026Article
- Benchmarking Docking Protocols on Predicting Alternative Binding Modes.Journal of chemical information and modeling · 2026Article
- ScrambleBench: a workflow for comparative assessment of structure-based de novo generative models.Journal of cheminformatics · 2026Article
- In silico screening for safe and potent essential oils against mosquito neural targets.Frontiers in zoology · 2026Article
- Small Molecule Liver X Receptor Modulator GAC0001E5 Targets Mechanisms of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer Cells.Biomolecules · 2026Article
- CholBindNet as an interpretable neural network for cholesterol-binding site classification.Communications chemistry · 2026Article
- ARumenamides as Multitarget Ion Channel Modulators: Insights from Fenestration-Focused Docking, ADMET Profiling, and Molecular Dynamics.International journal of molecular sciences · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
Molecule parametrization is an essential requirement to guarantee the accuracy of docking calculations. Parametrization includes a proper perception of chemical properties such as bonds, formal charges and protonation states. This includes large biological macromolecules, such as proteins and nucleic acids, and small molecules, such as ligands and cofactors. The structures of proteins and nucleic acids are challenging due to omission of several atoms from the structural model, and from the lack of connectivity and bond order information in the PDB and mmCIF file formats. For small molecules, the very large chemical diversity poses challenges for both validating correctness and providing accurate parameters. These challenges affect various modeling approaches like molecular docking and molecular dynamics. Moreover, several specialized methods (particularly in molecular docking) leverage specific chemical properties to add custom potentials, pseudoatoms, or manipulate atomic connectivity. To address these challenges, we developed Meeko, a molecular parametrization Python package that leverages the widely used RDKit cheminformatics library for a chemically accurate description of the molecular representation. Small molecules are modeled as single RDKit molecules, and biological macromolecules as multiple RDKit molecules, one for each residue. Meeko is highly customizable and designed to be easily scriptable for high-throughput processing, replacing MGLTools for receptor and ligand preparation.
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.