ProPores2: Web Service and Stand-Alone Tool for Identifying, Manipulating, and Visualizing Pores in Protein Structures

Abstract

Surface pockets, cavities, and tunnels in the 3D structures of proteins play integral functional roles such as enabling enzymatic catalysis, ligand binding, or transport of ions or small molecules across biomembranes. ProPores2 facilitates understanding and analysis of these processes by identifying pores and lining residues, determining their axes, and opening closed connections via side-chain rotation. The fast stand-alone tool introduces a novel mode for pore identification, improved axis determination, and additional features such as parallel batch processing and a graphical user interface. The new web service features an integrated and customizable protein viewer with an option to analyze and view more than one structure at once. This feature facilitates side-by-side comparisons of pores in different conformations of the same protein or of identified pores before and after opening gates within the same protein. ProPores2 is freely and publicly available at https://service.bioinformatik.uni-saarland.de/propores.