Chanalyzer: A Computational Geometry Approach for the Analysis of Protein Channel Shape and Dynamics.

ABSTRACT: Morphological analysis of protein channels is a key step for a thorough understanding of their biological function and mechanism. In this respect, molecular dynamics (MD) is a very powerful tool, enabling the description of relevant biological events at the atomic level, which might elude experimental observations, and pointing to the molecular determinants thereof. In this work, we present a computational geometry-based approach for the characterization of the shape and dynamics of biological ion channels or pores to be used in combination with MD trajectories. This technique relies on the earliest works of Edelsbrunner and on the NanoShaper software, which makes use of the alpha shape theory to build the solvent-excluded surface of a molecular system in an aqueous solution. In this frame

SUBMITTER: Raffo A 

PROVIDER: S-EPMC9358003 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature