ArticleIEEE/ACM transactions on computational biology and bioinformatics
Intensity-based skeletonization of CryoEM gray-scale images using a true segmentation-free algorithm.
Article in IEEE/ACM transactions on computational biology and bioinformatics. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 18 citations in OpenAlex.
- Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies.Molecules (Basel, Switzerland) · 2021Article
- Combine Cryo-EM Density Map and Residue Contact for Protein Structure Prediction - A Case Study.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2020Article
- Analytical Approaches to Improve Accuracy in Solving the Protein Topology Problem.Molecules (Basel, Switzerland) · 2018Article
- An Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map.Molecular based mathematical biology · 2017Article
- CHALLENGES IN MATCHING SECONDARY STRUCTURES IN CRYO-EM: AN EXPLORATION.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2016Article
- Constrained Cyclic Coordinate Descent for Cryo-EM Images at Medium Resolutions: Beyond the Protein Loop Closure Problem.Robotica · 2016Article
- Numerical geometry of map and model assessment.Journal of structural biology · 2015Article
- An Effective Computational Method Incorporating Multiple Secondary Structure Predictions in Topology Determination for Cryo-EM Images.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the image can be captured using a single segmentation. In this paper, we present a segmentation-free approach to extract the gray-scale curve-like skeletons. The approach relies on a novel representation of the 3D image, where the image is modeled as a graph and a set of volume trees. A test containing 36 synthesized maps and one authentic map shows that our approach can improve the performance of the two tested tools used in de novo modeling. The improvements were 62 and 13 percent for Gorgon and DP-TOSS, respectively.
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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.