Bridging the information gap: computational tools for intermediate resolution structure interpretation.

By Wen Jiang, Matthew L. Baker, Steven J. Ludtke, Wah Chiu. Journal of Molecular Biology, 2001

326 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8550e975dda60b04c7c7467e173d6f1fbaead440

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions (2010, unknown): “, 2002), Foldhunter (Jiang et al., 2001), FRM (Kovacs et al.”
Solvent accessible surface area approximations for rapid and accurate protein structure prediction (2009, methodology): “…methods to predict the structure for such proteins and to assist in structure elucidation from sparse or low-resolution experimental data generated by complementary techniques such as electron paramagnetic resonance spectroscopy [4], x-ray crystallography [5], and cryo-electron microscopy [5].”
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison (2002, methodology): “Likewise, the ability of MAMMOTH to detect structural similarities using query substructures or building blocks can be of interest in approaches aimed at fitting models to electron density maps using databases of known protein structures (Diller et al. 1999a,b; Perrakis et al. 1999; Lamzin and Perra”
Blind deconvolution in scientific imaging & computational photography (2011, methodology): “9 D-F display the molecular structure, the simulated density at a resolution of 8 Å and the fit of 1AHS into 2BTV provided by FOLDHUNTER (Jiang et al., 2001).”
De Novo Modeling in Cryo-EM Density Maps with Pathwalking (2016, background): “In addition, lower resolution annotations, such as secondary structure localization [18] [19] and domain segmentation [20] [21], can also be used gain insight into macromolecular structure and function despite the lack of atomic detail [22] [23] [24].”
Interactive motif and fold recognition in protein structures (2002, methodology): “Recently, Jiang et al. (2001) described the use of DEJAVU as the `fold-identi®cation engine' in their procedure to interpret low-resolution (6±12 AÊ ) cryo-EM maps.”
Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “One of the earliest software systems to detect biomolecular elements is Helixhunter.”
Constructing and Validating Initial Cα Models from Subnanometer Resolution Density Maps with Pathwalking (2012, background): “At subnanometer resolutions, secondary structure elements (SSE) become visible, with α - helices appearing as cylinders and β -sheets appearing as thin surfaces (Baker, Ju and Chiu, 2007; Jiang et al., 2001).”
EMAN2: an extensible image processing suite for electron microscopy. (2007, methodology): “, 2003), as well as several software packages designed speciWcally for this task (Jiang et al., 2001; Volkmann and Hanein, 1999; Wriggers et al., 1999).”