Recent developments in the CCP-EM software suite

By Tom Burnley, Colin M. Palmer, Martyn D. Winn. 2017

307 citations recorded by the source corpus.

An overview is given of the new CCP-EM software suite, including the underpinning framework, the current functionality and the distribution procedure. This first version of the suite has a focus on building and refining atomic models.

Subfields: Molecular Biology, Structural Biology, Surfaces, Coatings and Films

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In Molecular Biology

In Structural Biology

In Surfaces, Coatings and Films

Citations in the corpus

The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands (2022, positive): “For the p3dsRNA:RIG-I complex, PDB ID 5F9H was used as the initial search model for building into the cryo-EM map, using molrep in the ccpem software suit (Burnley et al., 2017; Devarkar et al., 2016).”
Automated map sharpening by maximization of detail and connectivity (2018, background): “Burnley et al. (2017) have recently noted that the challenge of optimizing map sharpening is an open one with the comment that, “Presently, the optimum sharpening coefficient (where ‘optimum’ means maximizing the interpretable density features) cannot be analytically determined either locally or…”
New tools for automated cryo-EM single-particle analysis in RELION-4.0 (2021, methodology): “0 release also introduces new approaches to sub-tomogram averaging, and a tighter integration of its pipeline approach with the CCP-EM software suite [53].”
Current approaches for automated model building into cryo-EM maps using Buccaneer with CCP-EM (2020, methodology): “CCP-EM The automated model-building pipeline within the CCPEM interface (Burnley et al., 2017) consists of several subtasks, as shown in Fig.”
Structure of the class D GPCR Ste2 dimer coupled to two G proteins (2020, unknown): “Thermostability measurements were performed on a Prometheus NanoTemper NT.48 and the data was analysed in PR.ThermControl v2.”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “In this contribution, we review the tools available for macromolecular structure refinement into cryo-EM reconstructions that are available via CCP-EM (Burnley et al., 2017).”
Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “Flex-EM can now be run via the CCP-EM suite.(169) Newer developments in MD-based methods such as CDMD(157) use an effective potential that maximizes this correlation rather than bias directly toward the density itself.”