GEO-Nav: a geometric dataset of voltage-gated sodium channels

TL;DR

GEO-Nav provides a detailed geometric dataset of mammalian voltage-gated sodium channels, facilitating drug discovery and morphological analysis by offering multiple representations and geometric measures.

Contribution

This work introduces a comprehensive geometric dataset of Nav channels with multiple representations and measures, filling a gap in drug design resources.

Findings

GEO-Nav enables effective morphological analysis of Nav channels.

The dataset supports different computational approaches.

Demonstrated utility on sphere-based and tessellation-based methods.

Abstract

Voltage-gated sodium (Nav) channels constitute a prime target for drug design and discovery, given their implication in various diseases such as epilepsy, migraine and ataxia to name a few. In this regard, performing morphological analysis is a crucial step in comprehensively understanding their biological function and mechanism, as well as in uncovering subtle details of their mechanism that may be elusive to experimental observations. Despite their tremendous therapeutic potential, drug design resources are deficient, particularly in terms of accurate and comprehensive geometric information. This paper presents a geometric dataset of molecular surfaces that are representative of Nav channels in mammals. For each structure we provide three representations and a number of geometric measures, including length, volume and straightness of the recognized channels. To demonstrate the effective use of GEO-Nav, we have tested it on two methods belonging to two different categories of approaches: a sphere-based and a tessellation-based method.