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