Computational protocol: Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes

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Protocol publication

[…] The structures of the complexes were solved by molecular replacement with the program PHASER (). The domains of the Ago-21-mer guide DNA binary complex structure () without the linkers were used as search models. Model building was done using COOT (), and refinement was done with CNS () and PHENIX (). The final Figures were created with Pymol (http://pymol.sourceforget.net/). The refinement statistics for all the Ago mutants and wild-type complexes are summarized in . […]

Pipeline specifications

Software tools Coot, CNS, PHENIX, PyMOL
Application Protein structure analysis
Organisms Thermus thermophilus
Chemicals Phosphates