Introducing Hippy: A visualization tool for understanding the α-helix pair interface Robert Fraser and Janice Glasgow School of Computing, Queen’s University, Kingston ON, Canada, K7L3N6 {robert,janice}@cs.queensu.ca ABSTRACT Hippy is a novel protein visualization tool de- signed to meet the needs of those who are work- ing with contact maps for protein structure prediction, and in particular for those desir- ing to gain insight into the configurations and properties of pairs of alpha helices. It is the only known program that allows the simulta- neous display of the structure and the contact map. Users can customize Hippy to display the side chains, contacts, and the steric surface of the helices. The program is open source; the software was implemented in OpenGL with an aim for platform independence. Keywords: Alpha helix, contact maps, pro- tein visualization, supersecondary strucutres 1. INTRODUCTION The 3D structure of a protein is primarily determined by the supersecondary structures present. The alpha helix is the most common type of secondary structure, as over a third of residues in globular proteins are found in he- lices. For this reason, alpha helices have been the subject of significant research. The inter- face between helix pairs is insufficiently under- stood for a prediction of the spatial configura- tion of a pair of helices ab initio. Many packing models have been developed, such as ‘knobs into holes’ 4 and ‘ridges into grooves’. 3 Al- though these models are illustrative, they fail Correspondence to: Robert Fraser Mail: School of Computing, Queen’s University, Kingston ON, Canada, K7L3N6 Email: robert@cs.queensu.ca to thoroughly describe the nature of interheli- cal interaction. The ability to predict the configuration of pairs of alpha helices would be an asset for protein structure prediction. It is the first step in a bottom-up approach for assembling sub- structures into a full tertiary structure for a protein. Our research is one component in a novel approach to protein structure prediction in which first a contact map is predicted for the protein from the primary sequence. 5 The tertiary structure is next predicted from the contact map using the bottom-up approach. 6 The present goal is to gain a thorough under- standing of the properties of the alpha helix pair and its corresponding contact map to aid in this study. 2. PROTEIN VISUALIZATION There exists a significant number of software packages designed for modelling proteins, most of which accept a Protein Data Bank (PDB) 2 format file for the protein as input and ex- tract the relevant information from the file. Among the most popular packages are Ras- mol, 16 Chimera, 15 Swiss-PDB viewer, 7 and Protein Explorer. 13 WebMol 18 is a visualiza- tion package that allows users to view and in- teract with the distance map for a protein; it is the only application with this feature that was found. Unfortunately, there is no option for displaying the contact map rather than the distance map. The limitation of all these pack- ages with regards to the applications consid- ered for this research is that the displays are tailored for the entire protein and do not allow for much insight into the interaction between