you, Professor Thayer, for your unending support and mentorship since our first meeting. I would also like to thank Professor Weir, Professor Langley, Professor Beveridge, and all the members of the Molecules2Medicine group for their feedback and guidance over the last four semesters. Your feedback has been invaluable throughout this process. This thesis would also not have been possible without all of Wesleyan's HPC resources -I would also like to thank Henk Meij for maintaining our cluster and for the HPC support.My family has always encouraged my love of learning, and their encouragement to pursue my interests has guided me through this process. I would like to thank my parents for their perpetual support in all areas of my education and my brother for at least feigning interest in my research.The residents of 7 Vine Street have heard me babble on and on about my research, and I cannot thank them enough for listening to me think out loud. I would especially like to thank Maya, who has now had the pleasure of listening to me talk about my simulations in multiple residences.iii I am grateful to have such supportive friends. Thank you to Adelaide and Josh, who have been so close to me throughout this process despite being so physically far away. I must also thank Magda and Lilley, my writing partners throughout this process, for keeping me motivated and keeping me company while writing. Thank you to all the members of the coding couch for being part of my CS community.