ArticleNature communications2021
Assessment of protein-protein interfaces in cryo-EM derived assemblies.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- MultilevelCurrent research in structural biology · 2026Article
- A shark variable new antigen receptor recognizes an occluded epitope of fibroblast activation protein.bioRxiv : the preprint server for biology · 2026Article
- PPIscreenML is a method for structure-based screening of protein-protein interactions using AlphaFold.eLife · 2026Article
- Protein-Protein Interactions as Promising Molecular Targets for Novel Antimicrobials Aimed at Gram-Negative Bacteria.International journal of molecular sciences · 2025Review
- AlphaPulldown2-a general pipeline for high-throughput structural modeling.Bioinformatics (Oxford, England) · 2025Article
- A ribosome-associating chaperone mediates GTP-driven vectorial folding of nascent eEF1A.Nature communications · 2025Article
- Review of protein structure-based analyses that illuminate plant stress mechanisms.Computational and structural biotechnology journal · 2025Review
- PPIFold: a tool for analysis of protein-protein interaction from AlphaPullDown.Bioinformatics advances · 2025Article
- AlphaPPIweb: an integration platform for protein-protein interaction prediction and evaluation.American journal of cancer research · 2025Article
- Engineering Streptomyces coelicolor for heterologous expression of the thiopeptide GE2270A-A cautionary tale.Journal of industrial microbiology & biotechnology · 2024Article
- Glucose-6-phosphate dehydrogenase and its 3D structures from crystallography and electron cryo-microscopy.Acta crystallographica. Section F, Structural biology communications · 2024Review
- An Ensemble Classifiers for Improved Prediction of Native-Non-Native Protein-Protein Interaction.International journal of molecular sciences · 2024Article
- AlphaCRV: a pipeline for identifying accurate binder topologies in mass-modeling with AlphaFold.Bioinformatics advances · 2024Article
- RNA to Rule Them All: Critical Steps in Lassa Virus Ribonucleoparticle Assembly and Recruitment.Journal of the American Chemical Society · 2023Article
- Molecular basis of TASL recruitment by the peptide/histidine transporter 1, PHT1.Nature communications · 2023Article
- AlphaPulldown-a python package for protein-protein interaction screens using AlphaFold-Multimer.Bioinformatics (Oxford, England) · 2023Article
- Overview and applications of map and model validation tools in the CCP-EM software suite.Faraday discussions · 2022Review
- Cryo-electron Microscopy of Adeno-associated Virus.Chemical reviews · 2022Review
- Cryo-EM reveals mechanisms of angiotensin I-converting enzyme allostery and dimerization.The EMBO journal · 2022Article
- Atomic model validation using the CCP-EM software suite.Acta crystallographica. Section D, Structural biology · 2022Article
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Authors and funding
4 authors.
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Abstract
Structures of macromolecular assemblies derived from cryo-EM maps often contain errors that become more abundant with decreasing resolution. Despite efforts in the cryo-EM community to develop metrics for map and atomistic model validation, thus far, no specific scoring metrics have been applied systematically to assess the interface between the assembly subunits. Here, we comprehensively assessed protein-protein interfaces in macromolecular assemblies derived by cryo-EM. To this end, we developed Protein Interface-score (PI-score), a density-independent machine learning-based metric, trained using the features of protein-protein interfaces in crystal structures. We evaluated 5873 interfaces in 1053 PDB-deposited cryo-EM models (including SARS-CoV-2 complexes), as well as the models submitted to CASP13 cryo-EM targets and the EM model challenge. We further inspected the interfaces associated with low-scores and found that some of those, especially in intermediate-to-low resolution (worse than 4 Å) structures, were not captured by density-based assessment scores. A combined score incorporating PI-score and fit-to-density score showed discriminatory power, allowing our method to provide a powerful complementary assessment tool for the ever-increasing number of complexes solved by cryo-EM.
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