• Dissertations
• 1. Canner, Samuel W "The Protein Sugar Interactome" (2025) Online.
  2. Harmalkar, Ameya "Computational Modeling, Prediction and Design of Protein-Protein Interactions" (2023) Online.
  3. Nance, Morgan "Modeling Protein–Carbohydrate Complexes in Rosetta" (2023) Online.
  4. Ruffolo, Jeff "Deep Learning Methods for Antibody Structure Prediction and Design" (2023) Online.
  5. Alford, Rebecca "Toward Biologically Realistic Computational Membrane Protein Structure Prediction and Design" (2020) Online.
  6. Jeliazkov, Jeliazko "Computational Modeling and Design of Protein-Protein Interations" (2019) Online.
  7. Roy Burman, Shourya S. "Modeling Interactions of Flexible Proteins" (2018).
  8. Marze, Nicholas "Building Computational Tools for Antibody Modeling and Protein-Protein Docking" (2017) Online.
  9. Pacella, Michael S. "Modeling and Design of Peptides to Control Biomineral Nucleation and Growth" (2017) Online.
  10. Kilambi, Krishna "Computational Prediction of Protein-Protein Interactions" (2015) Online.
  11. Weitzer, Brian D. "Next-Generation Antibody Modeling" (2015) Online.
  12. Berrondo, Monica "Predicting the structure and function of protein mutants" (2010) Online.
  13. Chaudhury, Sidhartha "Using computational protein docking to model the structure and specificity of protein interactions" (2010) Online.
  14. Sircar, Aroop "Computational antibody structure prediction and antibody-antigen docking" (2010) Online.
  15. Masica, Daivd L. "Structure determination and design of biomineral-associated proteins" (2009) Online.
  16. Daily, Michael D. "Systematic analysis of motions and communication networks in a benchmark set of allosteric proteins" (2008) Online.
• Master's Theses
• 1. Wei, Sen "Rosetta Energy Approximation using a Machine Learning Approach" (2024) Online.
  2. Gao, Wenhao "Development of a Protein Folding Environment for Reinforcement Learning" (2020) Online.
  3. Lasher, Brittany "Furthering Multiscale Membrane Protein Predicition and Design Approaches" (2019) Online.
  4. Biswas, Naireeta "Structural modelling of the Resistin family proteins and their cognate antibodies" (2017) Online.
  5. Long, Xiyao "Improving Antibody CDR Template Selection by Structural Cluster Prediction" (2017) Online.
  6. Lubin, Joseph H. "A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces" (2017) Online.
  7. Zuo, Xiaotong "Computational modeling of the C-terminal glycan of Type IV Pilin" (2016) Online.
  8. Muthu, Pravin "A comparison of sequence and structure-based approaches for enzyme specificity design" (2011).
  9. Guo, Lian "Docking HPr to HPr kinase with partial backbone flexibility" (2004) Online.
• Bachelor's Honors Theses
• 1. Porter, Justin R. "The selection of near-native decoys in protein-protein docking by score combinations using the Rosetta all-atom force field" (2012) Online.