Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations. - Subha Kalyaanamoorthy; Yi-Ping Phoebe Chen (J. Chem. Inf. Model., 2012)

Ligand release mechanisms and channels in histone deacetylases. - Subha Kalyaanamoorthy; Yi-Ping Phoebe Chen (J. Comput. Chem., 2013)

PoseFilter: a PyMOL plugin for filtering and analyzing small molecule docking in symmetric binding sites. - Justine C. Williams; Subha Kalyaanamoorthy (Bioinform., 2021)

Zero-shot transfer of protein sequence likelihood models to thermostability prediction. - Shawn Reeves; Subha Kalyaanamoorthy (Nat. Mac. Intell., 2024)

Revealing the impact of active site residues in modeling the inhibition mechanism of SARS-Cov-2 main protease by GC373. - Mohamed M. Aboelnga; Maya Petgrave; Subha Kalyaanamoorthy; Aravindhan Ganesan (Comput. Biol. Medicine, 2025)

Impact of Phosphorylation and O-GlcNAcylation on the Binding Affinity of R4 Tau Peptide to Microtubule and Its Conformational Preference upon Dissociation. - Sathish Dasari; Subha Kalyaanamoorthy (J. Chem. Inf. Model., 2025)

P4ward: An Automated Modeling Platform for Protac Ternary Complexes. - Paula Jofily; Subha Kalyaanamoorthy (J. Chem. Inf. Model., 2025)