ArticleBioinformatics (Oxford, England)2019
Automatic recognition of ligands in electron density by machine learning.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Structural and functional characterisation of the dextran utilisome fromJournal of structural biology: X · 2026Article
- Labeled dataset of X-ray protein ligand images in 3D point cloud and validated deep learning models.Scientific data · 2025Article
- A high-resolution data set of fatty acid-binding protein structures. III. Unexpectedly high occurrence of wrong ligands.Acta crystallographica. Section D, Structural biology · 2025Article
- Crystal structures of the putative endoribonuclease L-PSP from Entamoeba histolytica.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Structure of Plasmodium vivaxN-myristoyltransferase with inhibitor IMP-1088: exploring an NMT inhibitor for antimalarial therapy.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Ligand identification in CryoEM and X-ray maps using deep learning.Bioinformatics (Oxford, England) · 2024Article
- Ligand Identification in CryoEM and X-ray Maps Using Deep Learning.bioRxiv : the preprint server for biology · 2024Article
- Crystal structure of glutamyl-tRNA synthetase from Helicobacter pylori.Acta crystallographica. Section F, Structural biology communications · 2024Article
- Structures of Trichomonas vaginalis macrophage migratory inhibitory factor.Acta crystallographica. Section F, Structural biology communications · 2024Article
- Crystal structure of N-terminally hexahistidine-tagged Onchocerca volvulus macrophage migration inhibitory factor-1.Acta crystallographica. Section F, Structural biology communications · 2024Article
- InsPection of electron density maps supports wrongly modeled hexakisphosphate (InsP6) bound to African swine fever mRNA-decapping enzyme g5Rp.Journal of virology · 2024Article
- Continuous Validation Across Macromolecular Structure Determination Process.Nihon Kessho Gakkai shi · 2023Article
- Refolding of lid subdomain of SARS-CoV-2 nsp14 upon nsp10 interaction releases exonuclease activity.Structure (London, England : 1993) · 2022Article
- Molecular structure recognition by blob detection.RSC advances · 2021Article
- Detecting anomalies in X-ray diffraction images using convolutional neural networks.Expert systems with applications · 2021Article
- Recognizing and validating ligands with CheckMyBlob.Nucleic acids research · 2021Article
- Article
- Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models.Protein science : a publication of the Protein Society · 2021Article
- On the evolution of the quality of macromolecular models in the PDB.The FEBS journal · 2020Article
- MemBlob database and server for identifying transmembrane regions using cryo-EM maps.Bioinformatics (Oxford, England) · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Motivation: The correct identification of ligands in crystal structures of protein complexes is the cornerstone of structure-guided drug design. However, cognitive bias can sometimes mislead investigators into modeling fictitious compounds without solid support from the electron density maps. Ligand identification can be aided by automatic methods, but existing approaches are based on time-consuming iterative fitting. Results: Here we report a new machine learning algorithm called CheckMyBlob that identifies ligands from experimental electron density maps. In benchmark tests on portfolios of up to 219 931 ligand binding sites containing the 200 most popular ligands found in the Protein Data Bank, CheckMyBlob markedly outperforms the existing automatic methods for ligand identification, in some cases doubling the recognition rates, while requiring significantly less time. Our work shows that machine learning can improve the automation of structure modeling and significantly accelerate the drug screening process of macromolecule-ligand complexes. Availability and implementation: Code and data are available on GitHub at https://github.com/dabrze/CheckMyBlob. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.