All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. - Alexander D. MacKerell Jr.; Nilesh K. Banavali (J. Comput. Chem., 2000)

Structural Articulation of Biochemical Reactions Using Restrained Geometries and Topology Switching. - Swati R. Manjari; Nilesh K. Banavali (J. Chem. Inf. Model., 2018)

The Mechanism of Cholesterol Modification of Hedgehog Ligand. - Nilesh K. Banavali (J. Comput. Chem., 2020)

Celebrating Benoît Roux's 60th birthday: quantifying biology at the membrane. - Wonpil Im; Nilesh K. Banavali; Yun Lyna Luo (J. Comput. Chem., 2020)