Abstract
A new set of software tools has been developed for manipulating, visualizing, and quantifying properties of ion channels. ChannelTools is a plugin for the Visual Molecular Dynamics (VMD) program and brings together native VMD commands and several independent software routines in one simple graphical user interface. ChannelTools allows quick and easy visualization of ion channels and employs the HOLE program to visualize the channel pore and pore lining surface. An option to apply the atomic co-ordinate standardization previously developed by the authors is implemented yielding a consistent channel orientation, axis, and geometric centre. By employing the ESFERA program, pore volume and surface area can be computed from HOLE program output at the click of a button. Cross-sectional area and radius profile data and plots can also be generated with a single button click. Several different routines for estimating channel conductance are also being developed.
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