ArticleThe journal of physical chemistry. B2012
Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Advancing structure modeling from cryo-EM maps with deep learning.Biochemical Society transactions · 2025Review
- Secondary Structure Detection and Structure Modeling for Cryo-EM.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Protein complex structure modeling by cross-modal alignment between cryo-EM maps and protein sequences.Nature communications · 2024Article
- FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval.Genomics, proteomics & bioinformatics · 2024Article
- MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.Frontiers in molecular biosciences · 2022Article
- ZEAL: protein structure alignment based on shape similarity.Bioinformatics (Oxford, England) · 2021Article
- VESPER: global and local cryo-EM map alignment using local density vectors.Nature communications · 2021Article
- Protein Docking Model Evaluation by Graph Neural Networks.Frontiers in molecular biosciences · 2021Article
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- Article
- MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry.Journal of chemical information and modeling · 2020Article
- Protein docking model evaluation by 3D deep convolutional neural networks.Bioinformatics (Oxford, England) · 2020Article
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions.Nucleic acids research · 2019Article
- De novo main-chain modeling with MAINMAST in 2015/2016 EM Model Challenge.Journal of structural biology · 2018Article
- Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.Journal of molecular biology · 2018Article
- CryoEM-based hybrid modeling approaches for structure determination.Current opinion in microbiology · 2018Review
- De novo main-chain modeling for EM maps using MAINMAST.Nature communications · 2018Article
- Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.Frontiers in chemistry · 2018Review
- Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.Journal of structural biology · 2017Article
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2 authors.
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Abstract
A novel computational method for fitting high-resolution structures of multiple proteins into a cryoelectron microscopy map is presented. The method named EMLZerD generates a pool of candidate multiple protein docking conformations of component proteins, which are later compared with a provided electron microscopy (EM) density map to select the ones that fit well into the EM map. The comparison of docking conformations and the EM map is performed using the 3D Zernike descriptor (3DZD), a mathematical series expansion of three-dimensional functions. The 3DZD provides a unified representation of the surface shape of multimeric protein complex models and EM maps, which allows a convenient, fast quantitative comparison of the three-dimensional structural data. Out of 19 multimeric complexes tested, near native complex structures with a root-mean-square deviation of less than 2.5 Å were obtained for 14 cases while medium range resolution structures with correct topology were computed for the additional 5 cases.
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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.