About Me

I am an assistant professor at James Madison University in the computer science department. My research focuses on the development of novel algorithms for modeling complex systems. I am currently working in the field of computational protein design, specifically focusing on techniques to measure flexibility in different protein regions (which influences the docking with other molecular partners). My research goal is to develop algorithms to further our understanding of the roles proteins play in both healthy and unhealthy cells and to utilize this information to not just treat disease, but prevent disease. I am also investigating other disciplines (mainly robotics) to which these algorithms can be applied. I did my graduate work at George Mason University with Amarda Shehu (Shehu Computational Biology Lab). My PhD work focused on the development of algorithms to model protein systems, focusing on the complex relationship between protein sequence, structure, and dynamics. I completed an 18 month post-doctoral fellowship at CNRS-LAAS in Toulouse, France with Juan Cortés where I started to investigate different methods to model protein flexibility and algorithms to simultanously optimize design and motion.

Between my undergraduate and graduate studies, my wife and I established Molloy Software Associates (MSA) in 1997. MSA specializes in assisting businesses with very large Oracle databases (VLDBs). Specifically, we address issues with scalability, redundancy, and performance modeling (both analytical and benchmarking).

Other hobbies of mine include playing guitar (both classical and rock), cooking, aviation, photography, and sports (running, biking, swimming, triathlons).

Special Information on COVID-19

The computational structural biologists from around the globe are working on characterizing the dynamics and structure of the COVID-19 virus. I have been working on utilizing some of my work on this characterization as well. For your interest, here are some links to some of the larger labs and their findings/progress in this important investigation:

• Google's DeepMind Research Group
• CASP (Critical Assessment of Structure Prediction) Competition
• David Baker Lab (Rosetta)

Contact Info

email :	molloykp@jmu.edu
office :	ISAT/CS 216 Department of Computer Science 701 Carrier Drive, MSC 4103 Harrisonburg, VA 22807