Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL). - Daniel W. Kulp; Sabareesh Subramaniam; Jason E. Donald; Brett T. Hannigan; Benjamin K. Mueller; Gevorg Grigoryan; Alessandro Senes (J. Comput. Chem., 2012)

Expanding the toolkit for membrane protein modeling in Rosetta. - Julia Koehler Leman; Benjamin K. Mueller; Jeffrey J. Gray (Bioinform., 2017)

Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta. - Steven A. Combs; Benjamin K. Mueller; Jens Meiler (J. Chem. Inf. Model., 2018)