Identification of novel target sites and an inhibitor of the dengue virus E protein. - Ragothaman Yennamalli; Naidu Subbarao; Thorsten Kampmann; Ross P. McGeary; Paul R. Young; Bostjan Kobe (J. Comput. Aided Mol. Des., 2009)

Modified S-transform as a tool to identify secondary structure elements in RNA. - Nancy Singh; Sunil Datt Sharma; Ragothaman Yennamalli (Bio Algorithms Med Syst., 2017)

Protein Design. - Ragothaman Yennamalli (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Coarse grained modelling highlights the binding differences in the two different allosteric sites of the Human Kinesin EG5 and its implications in inhibitor design. - Soundarya Priya Alexandar; Ragothaman Yennamalli; Venkatasubramanian Ulaganathan (Comput. Biol. Chem., 2022)