STALK: An Interactive Virtual Molecular Docking System

Several recent technologies---genetic algorithms, parallel and distributed computing, virtual reality, and high-speed networking---provide the foundation for a new approach to the computational study of molecular interactions. Parallel genetic algorithms are an efficient and effective means to explore the large search spaces typical of these problems, while virtual reality provides an immersive environment for visualizing the interactions. In this paper we discuss the STALK system, which uses high-speed networking to couple a parallel genetic algorithm to a virtual reality environment. This combination allows a local or remote user to interact in real-time with the simulation through the virtual reality environment. Molecular docking experiments using an IBM SP parallel computer and a CAVE virtual reality environment are discussed. 1 Introduction A major challenge for computational biology is the development of efficient algorithms for determining the sites of interactions between mac..