CAREER: Intelligent Systems and Advanced Computation in Molecular Biology

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The aim of this project is to integrate research and education in advanced computation and artificial intelligence as applied to problems in molecular biology. The underlying research theme is the relation of structure to function in complex systems. The specific application focus is on enhanced protein structure prediction capability and its subsequent relation to function. Structural models and empirical objective functions are extracted from the existing scientific databases, thereby capitalizing on an enormous scientific investment compiled over decades. Structural predictions for novel protein sequences are made by aligning the sequence to the models so as to optimize the objective function. A novel branch and bound algorithm permits the true global optimum alignment to be found even though the underlying search problem is NP-hard. The education program creates a collaborative setting wherein computer scientists and biologists both can interact within an interdisciplinary research program. Students from both disciplines can get hands-on experience ``learning by doing'' research on real and important problems. The research will lead to improvements in our ability to predict protein structure and function from sequence, a crucial step toward design of novel pharmaceutical compounds, realizing the full potential of the human genome project, and understanding fundamental life processes.