VIPERdb: a relational database for structural virology. - Craig M. Shepherd; Ian A. Borelli; Gabriel Lander; Padmaja Natarajan; Vinay Siddavanahalli; Chandrajit L. Bajaj; John E. Johnson; Charles L. Brooks III; Vijay S. Reddy (Nucleic Acids Res., 2006)

VIPERdb2: an enhanced and web API enabled relational database for structural virology. - Mauricio Carrillo-Tripp; Craig M. Shepherd; Ian A. Borelli; Sangita Venkataraman; Gabriel Lander; Padmaja Natarajan; John E. Johnson; Charles L. Brooks III; Vijay S. Reddy (Nucleic Acids Res., 2009)

POSA: a user-driven, interactive multiple protein structure alignment server. - Zhanwen Li; Padmaja Natarajan; Yuzhen Ye; Thomas Hrabe; Adam Godzik (Nucleic Acids Res., 2014)

Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions. - Padmaja Natarajan; Marco Punta; Abhinav Kumar; Andrew P. Yeh; Adam Godzik; L. Aravind (BMC Bioinform., 2015)