Computational protocol: The Open Form Inducer Approach for Structure-Based Drug Design

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Protocol publication

[…] The crystal structure of TcDHODH in complex with compound 1 was solved by molecular replacement using the coordinates from TcDHODH-oxonate (2E6F)[] as the search model. For the remaining co-crystal structures of TcDHODH in open form, the coordinates from TcDHODH-compound 1 (3W1Q) was used. Manual building of the remaining model from TcDHODH and further crystallographic refinement were performed with the COOT[] and REFMAC5[] softwares. Data collection and structural refinement statistics are summarized in . Figures showing protein structures were prepared with the graphics programs PyMol (http://www.pymol.org/) and MOE[]. […]

Pipeline specifications

Software tools Coot, REFMAC5, PyMOL
Application Protein structure analysis
Organisms Trypanosoma cruzi