Docking structures of domains into maps from cryo-electron microscopy using local correlation.

By A. Roseman. 2000

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Citations in the corpus

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “A docking procedure is used if the model or a part of the model is already known (Roseman, 2000) but has not yet been placed into the map.”
Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy (2017, methodology): “Local cross correlation (SCCC) was introduced to avoid the influence of non-overlapping density in the calculations and quite a few developments that followed used this score (Roseman, 2000; Trabuco et al., 2008; Velazquez-Muriel et al., 2005).”
Recent developments in the CCP-EM software suite (2017, methodology): “Owing to the exhaustive nature of DockEM it is slower than MOLREP, but it is useful for low-resolution data sets where MOLREP cannot produce an unambiguous solution.”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “CCP-EM (Wood et al., 2015) contains various tools to facilitate model fitting/ refinement, including DockEM (Roseman, 2000), Choyce (Rawi et al., 2010) and Flex-EM (Joseph et al., 2016) for fitting and morphing of the structure at low resolution in cases where only information about the overall…”
Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions (2010, unknown): “, 2001), DOCKEM (Roseman, 2000), SITUS (Wriggers et al.”
TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows (2021, background): “There are different global scores available in TEMPy2 (Table 1) that include cross-correlation coefficient (CCC; Roseman, 2000), mutual information (MI; Vasishtan & Topf, 2011), least-squares fit (LSF; Vasishtan & Topf, 2011), normal vector scores (NV; Vasishtan & Topf, 2011) and envelope score…”
Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry (2016, methodology): “…structures for use as templates in molecular replacement (MR) techniques (Rossmann, 1990; Navaza, 2001), to provide angular parameters for locked MR search functions (Tong, 2001) or to dock high-resolution structural models into low-resolution cryo-EM density maps (Roseman, 2000), for example.”
Recent progress and future directions in protein-protein docking. (2008, methodology): “Although the ELSCA potential has not yet been used in predictive docking, it reproduces calculated PBSA energies of the 45 bound and unbound test complexes with correlation coefficients of 0.96 and 0.79, respectively.”
Scoring functions for cryoEM density fitting. (2011, methodology): “Other scores include variations on the CCF, such as the Local CCF (Roseman, 2000), Laplacian-filtered CCF (Chacon and Wriggers, 2002) and core-weighted CCF (Wu et al.”