Coot pipeline

Coot specifications

Information


Unique identifier OMICS_06370
Name Coot
Alternative name Crystallographic Object-Oriented Toolkit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Paul Emsley <>

Publications for Crystallographic Object-Oriented Toolkit

library_books

Handling ligands with Coot.

2012 Acta Crystallogr D Biol Crystallogr
PMID: 22505262
DOI: 10.1107/S0907444912000200

Coot citations

 (43)
2018
PMCID: 5834254

[…] available to researchers upon request to the corresponding authors., initial model of the chimeric reporter was built using the i-tasser server [63]. manual modeling operations were performed in coot [64] and molecular graphics were generated in pymol [65] [available at: http://www.pymol.org]., the primers were synthesized and page purified by idt dna. fugene 6 transfection reagent […]

2018
PMCID: 5845016

[…] with xds64. the crystal structure was determined by molecular replacement using the 14-3-3 epsilon structure (pdb: 2br9) as search model. manual model building and refinement were done with coot, ccp4 software suite, and phenix65–67. the final statistics of the refined models are shown in supplementary table 3., proteins were resolved on 4-12% gradient sds-page gels (nupage bis-tris […]

2018
PMCID: 5913127

[…] as the search model. the program molrep was used for both molecular replacement steps. well-defined electron density was observed for residues ala2 to asp7 of aβ1-11, which were manually built with coot59. no electron density was observed outside of the binding groove. aβ1-11 residues asp1, ser8 to glu11 could therefore not be built. structure refinement was performed using refmac560. the final […]

2017
PMCID: 5344670

[…] tmds and nbds, and in nbd1, that were not seen in our map. these regions were removed from the homology models before proceeding with refinement. the tm helices were then manually adjusted in coot, as a substantial adjustment was needed to move them into density. the domains were then refined in the same steps as outlined for kir6.2, except that before the final manual adjustments in coot […]

2017
PMCID: 5454536

[…] the ng loop of srp interacting with the ribosome was manually adjusted using the programme o6364. the kinked region of the srp rna and the signal sequence extension were manually modelled using coot65. homology models for the e. coli secy, sece and secg were generated using phyre2 (ref. 66) based on the x-ray structure of the isolated secyeg from t. thermophilus (pdb: 5ch4). the resulting […]

Coot institution(s)
Structure and Biophysics, DS, AstraZeneca, Alderley Park, Macclesfield, UK; Department of Biochemistry, University of Oxford, Oxford, UK
Coot funding source(s)
This project was funded by the Collaborative Computational Project Number 4.

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