PROTEIN FUNCTION PREDICTION BY INTEGRATING SEQUENCE, STRUCTURE AND BINDING AFFINITY INFORMATION

iii Dedicated to my parents. iv Acknowledgements I would never have been able to finish my dissertation without the guidance of my committee members, help from friends, and support from my family. I would like to express my deepest gratitude to my advisor, Prof Yaoqi Zhou, for his excellent guidance, caring, patience, and providing me with an excellent atmosphere for doing research. To my committee members Profs Yunlong Liu, Samy Meroueh, and Sarath Chandra Janga for their encouraging words, thoughtful criticisms, and time and attentions during busy semesters. To my colleagues for sharing their enthusiasm for and comments on my work