ArticleJournal of structural biology2012
Evolutionary bidirectional expansion for the tracing of alpha helices in cryo-electron microscopy reconstructions.
Article in Journal of structural biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Determining Protein Secondary Structures in Heterogeneous Medium-Resolution Cryo-EM Images Using CryoSSESeg.ACS omega · 2024Article
- The combined focal loss and dice loss function improves the segmentation of beta-sheets in medium-resolution cryo-electron-microscopy density maps.Bioinformatics advances · 2024Article
- An Approach to Developing Benchmark Datasets for Protein Secondary Structure Segmentation from Cryo-EM Density Maps.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2023Article
- The Combined Focal Cross Entropy and Dice Loss Function for Segmentation of Protein Secondary Structures from Cryo-EM 3D Density maps.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- Combining Cryo-EM Density Map and Residue Contact for Protein Secondary Structure Topologies.Molecules (Basel, Switzerland) · 2021Article
- A Tool for Segmentation of Secondary Structures in 3D Cryo-EM Density Map Components Using Deep Convolutional Neural Networks.Frontiers in bioinformatics · 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
- Using Curriculum Learning in Pattern Recognition of 3-dimensional Cryo-electron Microscopy Density Maps.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2020Article
- Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps.Journal of chemical information and modeling · 2020Article
- Simulation-Based Methods for Model Building and Refinement in Cryoelectron Microscopy.Journal of chemical information and modeling · 2020Review
- Exploratory Studies Detecting Secondary Structures in Medium Resolution 3D Cryo-EM Images Using Deep Convolutional Neural Networks.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2018Article
- A Pattern Recognition Tool for Medium-resolution Cryo-EM Density Maps and Low-resolution Cryo-ET Density maps.Bioinformatics research and applications : 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings. ISBRA (Conference) (14th : 2018 : Beijing, China) · 2018Article
- CryoEM-based hybrid modeling approaches for structure determination.Current opinion in microbiology · 2018Review
- Tracing Actin Filament Bundles in Three-Dimensional Electron Tomography Density Maps of Hair Cell Stereocilia.Molecules (Basel, Switzerland) · 2018Article
- Quantification of Twist from the Central Lines of β-Strands.Journal of computational biology : a journal of computational molecular cell biology · 2018Article
- Analysis of β-strand Twist from the 3-dimensional Image of a Protein.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2017Article
- Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps.BioMed research international · 2017Article
- An Iterative Bézier Method for Fitting Beta-sheet Component of a Cryo-EM Density Map.Molecular based mathematical biology · 2017Article
- Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Deep Convolutional Neural Networks for Detecting Secondary Structures in Protein Density Maps from Cryo-Electron Microscopy.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2016Article
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2 authors.
Funding
Abstract
Cryo-electron microscopy (cryo-EM) enables the imaging of macromolecular complexes in near-native environments at resolutions that often permit the visualization of secondary structure elements. For example, alpha helices frequently show consistent patterns in volumetric maps, exhibiting rod-like structures of high density. Here, we introduce VolTrac (Volume Tracer) - a novel technique for the annotation of alpha-helical density in cryo-EM data sets. VolTrac combines a genetic algorithm and a bidirectional expansion with a tabu search strategy to trace helical regions. Our method takes advantage of the stochastic search by using a genetic algorithm to identify optimal placements for a short cylindrical template, avoiding exploration of already characterized tabu regions. These placements are then utilized as starting positions for the adaptive bidirectional expansion that characterizes the curvature and length of the helical region. The method reliably predicted helices with seven or more residues in experimental and simulated maps at intermediate (4-10Å) resolution. The observed success rates, ranging from 70.6% to 100%, depended on the map resolution and validation parameters. For successful predictions, the helical axes were located within 2Å from known helical axes of atomic structures.
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