S. Hasnain, C. L. McClendon, M. T. Hsu, M. P. Jacobson, P. Bandyopadhyay.  “A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion”, PLoS One, 9 (2014) e0106466.  PMC4152264


L. X. Peng*, M. T. Hsu*, M. Bonomi, D. A. Agard, and M. P. Jacobson.  “The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery”, PLoS Computational Biology, 10 (2014) e1003464.  (* Joint first authors)  Open Access  PMC3916224


S. Hasnain, M. P. Jacobson, and P. Bandyopadhyay.  “A comparative Brownian dynamics investigation between small linear and circular DNA: Scaling of diffusion coefficient with size and topology of DNA”, Chemical Physics Letters, 591 (2014) 253-258.  Online


D. Datta, C. L. McClendon, M. P. Jacobson, and J. A. Wells.  “Substrate and inhibitor-induced dimerization and cooperativity in caspase-1 but not caspase-3”, Journal of Biological Chemistry, 288 (2013) 9971-9981.  PMC3617296


Z. Yu, M. P. Jacobson, and R. A. Friesner.  “What role do surfaces play in GB models? A new generation of surface-generalized Born model based on a novel Gaussian surface for biomolecules”, Journal of Computational Chemistry, 27 (2006) 72–89.  Online  PMC2743414


Z. Yu, M. P. Jacobson, C. S. Rapp, and R. A. Friesner.  “First-Shell Solvation of Ion Pairs:  Correction of Systematic Errors in Implicit Solvent Models”.  Journal of Physical Chemistry B, 108 (2004) 6643–6654.  Online


E. R. Jamieson, M. P. Jacobson, C. S. Chow, C. M. Barnes, and S. J. Lippard. “Fluorescence Resonance Energy Transfer Study of the Interaction of HMG1 Domain B with Cisplatin-Modified DNA”, Journal of Biological Chemistry, 274 (1999) 12346–12354.