Visualization of Protein 3D Structures in Reduced Representation with Simultaneous Display of Intra- and Inter-Molecular Interactions

Sheth, Vrunda, "Visualization of protein 3D structures in reduced representation with simultaneous display of intra and inter-molecular interactions" (2009). i This thesis is dedicated to my beloved family, to my parents for their never ending encouragement and confidence in me and to my sisters for their motivation and guidance. ii DISSERTATION AUTHOR PERMISSION STATEMENT TITLE OF THESIS: Visualization of protein 3D structure in a reduced representation with simultaneous display of intra and inter-molecular hydrogen bonds and van der Waals interactions. I, Vrunda Sheth, understand that I must submit a print copy of my thesis or dissertation to the RIT archives, per current RIT guidelines for the completion of my degree. I hereby grant to the Rochester Institute of Technology and its agents the non-exclusive license to archive and make accessible my thesis or dissertation in whole or in part in all forms of media in perpetuity. I retain all other ownership rights to the copyright of the thesis dissertation. I also retain the right to use in future works (such as articles or books) all or part of this thesis or dissertation. Date iii DISSERTATION PRINT REPRODUCTION PERMISSION STATEMENT TITLE OF THESIS: Visualization of protein 3D structure in a reduced representation with simultaneous display of intra and inter-molecular hydrogen bonds and van der Waals interactions. ACKNOWLEDGEMENTS I feel it is a unique privilege, combined with immense happiness, to acknowledge the contributions and support of all the wonderful people who have been responsible for the completion of my masters degree. The two years of graduate study at RIT has taught me that creative instinct, excellent fellowship and perceptiveness are the very essence of science. They not only impart knowledge but also place emphasis on the overall development of an individual. I am extremely appreciative of RIT, especially the Department of Biological Sciences (Bioinformatics Options) in this regard. I owe it to my mentors at RIT to what I am today. I would like to express my deepest gratitude to my thesis advisor, Dr Vicente Reyes who continually encouraged and guided me during the course of my thesis work. I would also like to express my appreciation to my committee members, Dr. Gary Skuse and Dr. Paul Craig for their valuable guidance, timely help and support. I would also like to thank Dr. Gurcharan Khanna, Ryan Lewis, Thomas Batzold and all other members of RIT Research Collaboratory for allowing me to use …