Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data
By A. Casañal, B. Lohkamp, P. Emsley. 2019
756 citations recorded by the source corpus.
Coot is a tool widely used for model building, refinement, and validation of macromolecular structures. It has been extensively used for crystallography and, more recently, improvements have been introduced to aid in cryo‐EM model building and refinement, as cryo‐EM structures with resolution ranging 2.5–4 A are now routinely available. Model building into these maps can be time‐consuming and requires experience in both biochemistry and building into low‐resolution maps. To simplify and expedite the model building task, and minimize the needed expertise, new tools are being added in Coot. Some examples include morphing, Geman‐McClure restraints, full‐chain refinement, and Fourier‐model based residue‐type‐specific Ramachandran restraints. Here, we present the current state‐of‐the‐art in Coot usage.
Subfields: Materials Chemistry, Molecular Biology, Structural Biology
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In Materials Chemistry
- Andriy Kryshtafovych
- Maya Topf
- Daniel J. Rigden
- Rhiju Das
- Thomas Mulvaney
- J. Beton
- Tristan Cragnolini
- Rachael Kretsch
In Molecular Biology
- Andriy Kryshtafovych
- Maya Topf
- Daniel J. Rigden
- Rhiju Das
- Thomas Mulvaney
- J. Beton
- Tristan Cragnolini
- Rachael Kretsch
In Structural Biology
Citations in the corpus
- CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps (2023, methodology): “However, the model provided by Wallner (group 037) was by visual inspection close and could potentially be locally fitted and refined using interactive tools such as Coot 32 or ISOLDE 33 .”
- Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “Tools such as Coot 143 aid this manual validation and fitting process and offer tools for fixing incorrectly modeled regions such as jiggle-fit 185 and bac-krub.”