MATCH: An atom-typing toolset for molecular mechanics force fields. - Joseph D. Yesselman; Daniel J. Price; Jennifer L. Knight; Charles L. Brooks III (J. Comput. Chem., 2012)

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. - Jennifer L. Knight; Joseph D. Yesselman; Charles L. Brooks III (J. Comput. Chem., 2013)

Primerize: automated primer assembly for transcribing non-coding RNA domains. - Siqi Tian; Joseph D. Yesselman; Pablo Cordero; Rhiju Das (Nucleic Acids Res., 2015)

RNA-Redesign: a web server for fixed-backbone 3D design of RNA. - Joseph D. Yesselman; Rhiju Das (Nucleic Acids Res., 2015)

Updates to the RNA mapping database (RMDB), version 2. - Joseph D. Yesselman; Siqi Tian; Xin Liu 028; Lei Shi; Jin Billy Li; Rhiju Das (Nucleic Acids Res., 2018)

Web-based platform for analysis of RNA folding from high throughput chemical probing data. - Christopher P. Jurich; Amir Brivanlou; Silvi Rouskin; Joseph D. Yesselman (Nucleic Acids Res., 2022)