ion-channel

A MATLAB neuron simulator. Very fast (written in C++). Flexible (fully object oriented). Immediate (live manipulation in MATLAB). Comes with a powerful parameter optimizer. Get started ➡️

CHAP is a tool for the functional annotation of ion channel structures:

Alchemical Free Energy Calculations with Grand Canonical Ensemble

imaging, spike trains, information theory, neural circuitry, synaptic, channel properties

Cardiac Action Potential Prediction (ApPredict) under drug-induced block of ion channels. This is a Chaste extension/bolt-on project.

Code for training and validation of ion channel models fitted to sine-wave based voltage clamp data

Simulation code and data reproducing "An Open-Quantum-Systems Theory of Quantum-Biological Communication Channels" (IEEE TMBMC).

Fit rates in an ion channel gating mechanism to idealized openings and closings.

Interactive, physics-driven 3D simulator of the IP3 receptor: C4 elastic-network modes, De Young-Keizer gating and Ca2+ dynamics, and independent re-derivation of the ip3r_genes findings.

Reverse Engineering the Gate Composition given the Voltage Trace of a Gate

Computational pipeline for prioritizing structurally tractable pharmacologic rescue candidates across KCNQ1-KCNQ5.

CHAP Docker image source files

In-silico structural & evolutionary characterisation of NKG7 (cytotoxic-lymphocyte granule tetraspan): structure prediction + homology + pore analysis. Tests the ion-channel hypothesis — finds a self-associating claudin/Ca_V-γ scaffold, not a pore.

Standardized, provenance-tracked context-graph objects for multi-omic biology - the substrate purpose-specific 'omic' models need. Validated on RYR1 variant-to-structure-and-function interpretation (malignant hyperthermia). Built with Claude Code + Claude Science.