High-resolution structure of a retroviral protease folded as a monomer

By M. Gilski, Maciej Kazmierczyk, S. Krzywda, Helena Zábranská, S. Cooper, Zoran Popovic, Firas Khatib, Frank DiMaio, James M. Thompson, David Baker and 2 more. 2011

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Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data (2019, methodology): “The most practical quality indicators are the Geometry analysis, Difference Map Peaks, Density-fit analysis, Rotamer analysis, and Ramachandran and Kleywegt plots.(2) These tools identify problematic regions in themodel and allow fast navigation for their resolution.”
OpenStructure: an integrated software framework for computational structural biology (2013, methodology): “Conceptually, the language is similar to the selection capabilities of other software packages, e.g. VMD (Humphrey et al., 1996), Coot (Emsley et al., 2010) or PyMOL (Schrodinger).”
Target Binding Properties and Cellular Activity of Afatinib (BIBW 2992), an Irreversible ErbB Family Blocker (2012, methodology): “Subsequent model building and refinement was performed according to standard protocols with the CCP4 (Collaborative Computational Project, Number 4, 1994) and COOT (Emsley et al., 2010) software packages.”
Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM (2018, methodology): “Several of the techniques available in Coot (Emsley et al., 2010) have successfully Acta Cryst.”
The 3.8Å resolution cryo-EM structure of Zika Virus (2016, methodology): “The atomic model was built manually using the program Coot (27) and refined with Phenix (28) and CNS (29).”