ArticleJournal of structural biology2011
Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes.
Article in Journal of structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
55 citing papers in PubMed, 84 citations in OpenAlex.
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- prM-reactive antibodies reveal a role for partially mature virions in dengue virus pathogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Cryo-ET ofProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Validation, analysis and annotation of cryo-EM structures.Acta crystallographica. Section D, Structural biology · 2021Article
- MAINMASTseg: Automated Map Segmentation Method for Cryo-EM Density Maps with Symmetry.Journal of chemical information and modeling · 2020Article
- Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.Molecules (Basel, Switzerland) · 2019Review
- Transportin-1 binds to the HIV-1 capsid via a nuclear localization signal and triggers uncoating.Nature microbiology · 2019Article
- Tracing Actin Filament Bundles in Three-Dimensional Electron Tomography Density Maps of Hair Cell Stereocilia.Molecules (Basel, Switzerland) · 2018Article
- Editorial: Hybrid Biomolecular Modeling.Frontiers in molecular biosciences · 2018Article
- Asymmetric Cryo-EM Structure of Anthrax Toxin Protective Antigen Pore with Lethal Factor N-Terminal Domain.Toxins · 2017Article
- ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.Science (New York, N.Y.) · 2017Article
- Flexible Fitting of Atomic Models into Cryo-EM Density Maps Guided by Helix Correspondences.Biophysical journal · 2017Article
- The Tetrameric Plant Lectin BanLec Neutralizes HIV through Bidentate Binding to Specific Viral Glycans.Structure (London, England : 1993) · 2017Article
- Crystallographic analysis of the laminin β2 short arm reveals how the LF domain is inserted into a regular array of LE domains.Matrix biology : journal of the International Society for Matrix Biology · 2017Article
- Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs.Nucleic acids research · 2016Article
- The N-terminal domain plays a crucial role in the structure of a full-length human mitochondrial Lon protease.Scientific reports · 2016Article
- Structure and Genome Release Mechanism of the Human Cardiovirus Saffold Virus 3.Journal of virology · 2016Article
- Constrained Cyclic Coordinate Descent for Cryo-EM Images at Medium Resolutions: Beyond the Protein Loop Closure Problem.Robotica · 2016Article
- Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
We describe an integrated software system called Sculptor that combines visualization capabilities with molecular modeling algorithms for the analysis of multi-scale data sets. Sculptor features extensive special purpose visualization techniques that are based on modern GPU programming and are capable of representing complex molecular assemblies in real-time. The integration of graphics and modeling offers several advantages. The user interface not only eases the usually steep learning curve of pure algorithmic techniques, but it also permits instant analysis and post-processing of results, as well as the integration of results from external software. Here, we implemented an interactive peak-selection strategy that enables the user to explore a preliminary score landscape generated by the colors tool of Situs. The interactive placement of components, one at a time, is advantageous for low-resolution or ambiguously shaped maps, which are sometimes difficult to interpret by the fully automatic peak selection of colors. For the subsequent refinement of the preliminary models resulting from both interactive and automatic peak selection, we have implemented a novel simultaneous multi-body docking in Sculptor and Situs that softly enforces shape complementarities between components using the normalization of the cross-correlation coefficient. The proposed techniques are freely available in Situs version 2.6 and Sculptor version 2.0.
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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.