The Channel Annotation Package

A new tool for the functional annotation of novel ion channel structures that provides information on the biophysical properties of the ion permeation pathway by utilising molecular dynamics simulations.

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What is CHAP?

With the discovery of novel ion channel structures continuing at an accelerated pace there is a need for improved tools that facilitate the functional annotation of these structures. The computational approach underlying CHAP is capable of rapidly identifying hydrophobic gates, i.e. energetic barriers to ion permeation that result from the dewetting of hydrophobic segments within the nanometre-sized pores found in most ion channels. Such hydrophobic barriers are not detectable by a simple measurement of the physical dimensions of a channel pore and it is now clear that they represent an important predictor of channel permeability.

Hydrophobic gating principle

Pore Hydration Analysis

CHAP goes beyond measurement of pore dimensions and facilitates an analysis of the hydration behaviour of a channel's permeation pathway. This permits fast identification of hydrophobic gates and thus improves the functional annotation of novel channel structures.

Based on Molecular Dynamics

CHAP makes use of the popular molecular dynamics engine Gromacs to derive the biophysical properties of a channel's permeation pathway and thereby relates channel structure and function.

Visualisation Included

CHAP allows the visualisation of properties of the channel pore in common molecular viewers like VMD and PyMOL. Scripts for plotting results using R and Python are also included.