Comparing pharmacophore models derived from crystallography and NMR ensembles. - Phani Ghanakota; Heather A. Carlson (J. Comput. Aided Mol. Des., 2017)

Large-Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at Protein-Protein Interaction Interfaces. - Phani Ghanakota; Herman van Vlijmen; Woody Sherman; Thijs Beuming (J. Chem. Inf. Model., 2018)

Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations. - Phani Ghanakota; Debarati DasGupta; Heather A. Carlson (J. Chem. Inf. Model., 2019)

Combining Cloud-Based Free-Energy Calculations, Synthetically Aware Enumerations, and Goal-Directed Generative Machine Learning for Rapid Large-Scale Chemical Exploration and Optimization. - Phani Ghanakota; Pieter H. Bos; Kyle D. Konze; Joshua Staker; Gabriel Marques; Kyle Marshall; Karl Leswing; Robert Abel; Sathesh Bhat (J. Chem. Inf. Model., 2020)

Predicting Resistance to Small Molecule Kinase Inhibitors. - Anu Nagarajan; Katherine Amberg-Johnson; Evan Paull; Kunling Huang; Phani Ghanakota; Asela Chandrasinghe; Jackson Chief Elk; Jared M. Sampson; Lingle Wang; Robert Abel; Steven K. Albanese (J. Chem. Inf. Model., 2025)