X. Y. He, Y. J. Li, C. Kalyanaraman, L. L. Qiu, C. Chen, Q. Xiao, W. X. Liu, W. Zhang, J. J. Yang, G. Chen, M. P. Jacobson, and Y. S. Shi.  “GluA1 signal peptide determines the spatial assembly of heteromeric AMPA receptors”, PNAS, 113 (2016) E5645-E5654.  PMC5035880



F. H. Wallrapp, J.-J. Pan, G. Ramamoorthy, D. E. Almonacid, B. S. Hillerich, R. Seidel, Y. Patskovsky, P. C. Babbitt, S. C. Almo, M. P. Jacobson and C. D. Poulter. “Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily”.  PNAS, 110 (2013) E1196-E1202.  Open access  PMC3612614


T. Lukk, A. Sakai, C. Kalyanaraman, S. Brown, H. J. Imker, L. Song, A. A. Fedorov, E. V. Fedorov, R. Toro, B. Hillerich, R. Seidel, Y. Patskovsky, M. W. Vetting, S. K. Nair, P. C. Babbitt, S. C. Almo, J. A. Gerlt, and M. P. Jacobson.  “Computational prediction of the diversity of enzyme specificity among dipeptide epimerases in the enolase superfamily”.  PNAS, 109 (2012) 4122-4127. [F1000] [Discussion in PSI/Nature Knowledgebase] [Chemical&Engineering News] PMC3306705


T. Schwede, A. Sali, B. Honig, M. Levitt, H. M. Berman, D. Jones, S. E. Brenner, S. K. Burley, R. Das, N. V. Dokholyan, R. L. Dunbrack Jr, K. Fidelis, A. Fiser, A. Godzik, C. Humblet, M. P. Jacobson, A. Joachimiak, S. R. Krystek Jr., T. Kortemme, A. Kryshtafovych, G. Montelione, J. Moult, D. Murray, R. Sanchez, T. R. Sosnick, D. M. Standley, T. Stouch, S. Vajda, M. Vasquez, J. D. Westbrook, and I. A. Wilson.  “Outcome of Workshop on Applications of Protein Models in Biomedical Research”, Structure, 13 (2009) 151–159.  PMC2739730


C. Kalyanaraman, H. J. Imker, A. A. Federov, E. V. Federov, M. E. Glasner, P. C. Babbitt, S. C. Almo, J. A. Gerlt, and M. P. Jacobson.  “Discovery of a new dipeptide epimerase enzymatic function guided by homology modeling and virtual screening”, Structure, 16 (2008) 1668–1677.  [Preview:  D. Dunaway-Mariano, “Enzyme Function Discovery“, 16 (2008) 1599–1600.]  Online  PMC2714228


L. Song, C. Kalyanaraman, A. A. Fedorov, E. V. Fedorov, M. E. Glasner, S. Brown, P. C. Babbitt, S. C. Almo, M. P. Jacobson, and J. A. Gerlt.  “Assignment and Prediction of Function in the Enolase Superfamily:  A Divergent N-Succinyl Amino Acid Racemase from Bacillus cereus“, Nature Chemical Biology, 3 (2007) 486–491.  [News&Views:  K. N. Allen, “Form finds function“, Nature Chemical Biology, 3 (2007) 452–453.]   [NIGMS “Biomedical Beat“]  F1000  Online


K. Zhu, M. R. Shirts, R. A. Friesner, and M. P. Jacobson.  “Multiscale Optimization of a Truncated Newton Minimization Algorithm and Applications to Proteins and Protein-Ligand Complexes”, Journal of Chemical Theory and Computation, 3 (2007) 640–648.  Online


X. Li, M. P. Jacobson, K. Zhu, S. Zhao, and R. A. Friesner.  “Assignment of Polar States for Protein Amino Acid Residues Using an Interaction Cluster Decomposition Algorithm and its Application to High Resolution Protein Structure Modeling”, Proteins, 66 (2007) 824–837.  Online  Pubmed


V. Guallar, M. P. Jacobson, A. McDermott, and R. A. Friesner. “Computational Modeling of the Catalytic Reaction in Triose Phosphate Isomerase”, Journal of Molecular Biology, 337 (2004) 227–239.


M. Andrec, Y. Harano, M. P. Jacobson, R. A. Friesner, and R. M. Levy. “Complete Protein Structure Determination Using Backbone Residual Dipolar Couplings and Sidechain Rotamer Prediction”, Journal of Structural and Functional Genomics, 2 (2002) 103–111.