| 2012 | PSB | Quasi-Anharmonic Analysis Reveals Intermediate States in the Nuclear Co-Activator Receptor Binding Domain Ensemble. | Virginia M. Burger, Arvind Ramanathan, Andrej J. Savol, Christopher B. Stanley, Pratul K. Agarwal, Chakra S. Chennubhotla |
| 2010 | SC | Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations. | Scott S. Hampton, Sadaf R. Alam, Paul S. Crozier, Pratul K. Agarwal |
| 2009 | RECOMB | An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations. | Arvind Ramanathan, Pratul K. Agarwal, Maria G. Kurnikova, Christopher James Langmead |
| 2008 | HiPC | Experimental Evaluation of Molecular Dynamics Simulations on Multi-core Systems. | Sadaf R. Alam, Pratul K. Agarwal, Scott S. Hampton, Hong Ong |
| 2007 | BIBE | Performance Evaluation of a Scalable Molecular Dynamics Simulation Framework on a Massively-Parallel System. | Sadaf R. Alam, Pratul K. Agarwal, Jeffery A. Kuehn |
| 2006 | PPoPP | Performance characterization of molecular dynamics techniques for biomolecular simulations. | Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwal, Al Geist |