In this project, based on applications in protein structure alignment and its visualization, we will investigate several fundamental problems regarding the discrete Frechet distance. These include improving the computation time for protein structure alignment by taking into account practical conditions (e.g. the lengths of the segments connecting neighboring alpha-carbon atoms are almost uniform), and simultaneously simplifying a pair of chains for realistic visualization, etc. Based on these theoretical investigations, we also plan to build a prototype software system, available in the public domain, for these applications.
Protein structure alignment is an important and fundamental technique used to understand the evolution of proteins and to predict their functionality. This understanding is crucial for the identification of the cause of certain diseases and for the development of new drugs. Here we propose a new approach based on the discrete Frechet distance to improve the quality and speed of protein structure alignment. Our proposal will consider fundamental questions with regard to this technique. The resulting software tools will be accessed by the public for education and research. This project will help support and train several graduate students at Montana State University.
