HelixFinder A program for identifying and classifying protein alpha-helix pairs

Abstract

To gain understanding of proteins and increase knowledge of how they interact with and impact each other, studying larger sets of data on proteins is important. Being able to easily aggregate such data is essential for this type of analysis. This work is investigating how to detect some specific sections of protein secondary structures,alpha-helices, and to, within a given protein, identify pairs of such helices that are close to each other. The identified pairs are categorized in four different categories, depending on how the distance is detected. The outcome is a program, HelixFinder, that detects such helix pairs and gathers information about them. The program uses an implementation of the DSSP algorithm to identify the structures, and a rotational algorithm together with a number of distance tests to identify alpha-helix pairs and output data relevant for further analysis.