ArticleActa crystallographica. Section D, Structural biology2020
Predicting protein model correctness in Coot using machine learning.
Article in Acta crystallographica. Section D, Structural biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Protein Science Meets Artificial Intelligence: A Systematic Review and a Biochemical Meta-Analysis of an Inter-Field.Frontiers in bioengineering and biotechnology · 2022Pooled it
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- Catalytic architecture and cyclase-mediated dimerization of a newly identified class III-c lanthipeptide synthetase.Protein science : a publication of the Protein Society · 2026Article
- Ultrapotent neutralization of Bacillus anthracis toxin by a human antibody via blockade of PA oligomerization.PLoS pathogens · 2026Article
- Pinpointing Protein Crystal Structures over a Broad Temperature Range Using Hydrophobic Protection.ACS omega · 2026Article
- Role of g5Rp in African swine fever virus replication: disruption of host translation and autophagy.Journal of virology · 2026Article
- Potent Cross-neutralizing Antibodies Reveal Vulnerabilities of Henipavirus Fusion Glycoprotein.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Leveraging core enzyme structures for microbiota targeted functional regulation: Urease as an example.iMeta · 2025Article
- Tamsulosin ameliorates bone loss by inhibiting the release of ClProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Integrating machine learning to advance epitope mapping.Frontiers in immunology · 2024Review
- Heterologous boost with mRNA vaccines against SARS-CoV-2 Delta/Omicron variants following an inactivated whole-virus vaccine.Antiviral research · 2023Article
- Buccaneer model building with neural network fragment selection.Acta crystallographica. Section D, Structural biology · 2023Article
- A Guide to In Silico Drug Design.Pharmaceutics · 2022Review
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- ModelCraft: an advanced automated model-building pipeline using Buccaneer.Acta crystallographica. Section D, Structural biology · 2022Article
- Predicting the performance of automated crystallographic model-building pipelines.Acta crystallographica. Section D, Structural biology · 2021Article
- Shift-field refinement of macromolecular atomic models.Acta crystallographica. Section D, Structural biology · 2020Article
- Structural barriers to scientific progress.Acta crystallographica. Section D, Structural biology · 2020Article
Corrections and comments
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3 authors.
Funding
Abstract
Manually identifying and correcting errors in protein models can be a slow process, but improvements in validation tools and automated model-building software can contribute to reducing this burden. This article presents a new correctness score that is produced by combining multiple sources of information using a neural network. The residues in 639 automatically built models were marked as correct or incorrect by comparing them with the coordinates deposited in the PDB. A number of features were also calculated for each residue using Coot, including map-to-model correlation, density values, B factors, clashes, Ramachandran scores, rotamer scores and resolution. Two neural networks were created using these features as inputs: one to predict the correctness of main-chain atoms and the other for side chains. The 639 structures were split into 511 that were used to train the neural networks and 128 that were used to test performance. The predicted correctness scores could correctly categorize 92.3% of the main-chain atoms and 87.6% of the side chains. A Coot ML Correctness script was written to display the scores in a graphical user interface as well as for the automatic pruning of chains, residues and side chains with low scores. The automatic pruning function was added to the CCP4i2 Buccaneer automated model-building pipeline, leading to significant improvements, especially for high-resolution structures.
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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.