ArticleJournal of structural biology2012
Real-space processing of helical filaments in SPARX.
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 26 papers.
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Who cites it
26 citing papers in PubMed.
- Article
- Toll-like receptor signaling outcome is determined by the stoichiometry of the endogenous TRIFosome.Science advances · 2026Article
- The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI.Biochemical Society transactions · 2022Article
- Automated picking of amyloid fibrils from cryo-EM images for helical reconstruction with RELION.Journal of structural biology · 2021Article
- Article
- TranSPHIRE: automated and feedback-optimized on-the-fly processing for cryo-EM.Nature communications · 2020Article
- Direct Visualization of Actin Filaments and Actin-Binding Proteins in Neuronal Cells.Frontiers in cell and developmental biology · 2020Review
- Structural basis for the clamping and CaNature communications · 2019Article
- Structural transitions of F-actin upon ATP hydrolysis at near-atomic resolution revealed by cryo-EM.Nature structural & molecular biology · 2018Article
- Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface.Science (New York, N.Y.) · 2018Article
- Automated tracing of helical assemblies from electron cryo-micrographs.Journal of structural biology · 2018Article
- Helical reconstruction in RELION.Journal of structural biology · 2017Article
- Molecular mechanism governing ratio-dependent transcription regulation in the ccdAB operon.Nucleic acids research · 2017Article
- The myosin X motor is optimized for movement on actin bundles.Nature communications · 2016Article
- Deducing the symmetry of helical assemblies: Applications to membrane proteins.Journal of structural biology · 2016Article
- Force-producing ADP state of myosin bound to actin.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Three-dimensional reconstruction of helical polymers.Archives of biochemistry and biophysics · 2015Review
- Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization.Journal of structural biology · 2015Article
- Structure and function of enterotoxigenic Escherichia coli fimbriae from differing assembly pathways.Molecular microbiology · 2015Article
- Site-specific cation release drives actin filament severing by vertebrate cofilin.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We present a major revision of the iterative helical real-space refinement (IHRSR) procedure and its implementation in the SPARX single particle image processing environment. We built on over a decade of experience with IHRSR helical structure determination and we took advantage of the flexible SPARX infrastructure to arrive at an implementation that offers ease of use, flexibility in designing helical structure determination strategy, and high computational efficiency. We introduced the 3D projection matching code which now is able to work with non-cubic volumes, the geometry better suited for long helical filaments, we enhanced procedures for establishing helical symmetry parameters, and we parallelized the code using distributed memory paradigm. Additional features include a graphical user interface that facilitates entering and editing of parameters controlling the structure determination strategy of the program. In addition, we present a novel approach to detect and evaluate structural heterogeneity due to conformer mixtures that takes advantage of helical structure redundancy.
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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.