In Silico Inositol Phosphate Docking

Docking studies were carried out with AutoDock4 (ref. 64 (link)), utilizing the AutoDockTools 1.5.6 GUI. Non-polar hydrogens and Gasteiger atomic charges were added to the HDAC3:SMRT DAD atomic coordinates (PDB ID: 4A69) in AutoDockTools. The inositol phosphate-binding site was as defined in ref. 2 (link). Probes were calculated at every 0.375 Å grid position of a grid box (box size x, y, z=21.406, 50.64, 23.036 Å, respectively), centred upon the inositol ring. The docking of the inositol phosphates was run using the Lamarckian genetic algorithm in AutoDock4. Other parameters were set to the default values.

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Watson P.J., Millard C.J., Riley A.M., Robertson N.S., Wright L.C., Godage H.Y., Cowley S.M., Jamieson A.G., Potter B.V, & Schwabe J.W. (2016). Insights into the activation mechanism of class I HDAC complexes by inositol phosphates. Nature Communications, 7, 11262.

Publication 2016

AutoDockTools

Binding site Hydrogens Inositol Inositol phosphates Lamarckian Smrt

Corresponding Organization :

Other organizations : Institute of Structural and Molecular Biology, University of Leicester, University of Bath, University of Oxford

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Variable analysis

independent variables

The docking of the inositol phosphates

dependent variables

Not explicitly mentioned

control variables

The HDAC3:SMRT DAD atomic coordinates (PDB ID: 4A69)
The inositol phosphate-binding site as defined in ref. 2
Grid box size (x, y, z = 21.406, 50.64, 23.036 Å, respectively), centered upon the inositol ring
Lamarckian genetic algorithm in AutoDock4
Default parameter values

positive controls

Not mentioned

negative controls

Not mentioned

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