Automated Protein Chain Isolation from 3D Cryo-EM Data and Volume Comparison Tool

Abstract

In electron cryo-microscopy (cryo-EM), manual isolation of volumetric protein density map data surrounding known protein structures is a time-consuming process that requires constant expert attention for multiple hours. This paper presents a tool, Volume Cut, and an algorithm to automatically isolate the volumetric data surrounding individual protein chains from the entire macro-molecular complex that runs in just minutes. This tool can be used in the data collection and data pre-processing steps to generate good training datasets of single chain volume-structure pairs, which can be further used for the study of protein structure prediction from experimental 3D cryo-EM density maps using data mining and machine learning. Additionally, an application of this tool was explored in depth that compares the cut experimental cryo-EM data with simulated data in an attempt to find irregularities of experimental data for the purpose of validation. The source for both tools can be found at https://github.com/nissensonm/VolumeCut/.