M. Armstrong, C. van Hoorebeke, T. Horn, J. Deschamps, J. C. Freedman, C. Kalyanaraman, M. P. Jacobson, and T. Holman.  “Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency”, Bioorg. Med. Chem., 24 (2016) 5380-5387.  PMC5065787



X. Zhang, M. S. Carter, M. W. Vetting, B. San Francisco, S. Zhao, N. F. Al-Obaidi, J. O. Solbiati, J. J. Thiaville, V. de Crécy-Lagard, M. P. Jacobson, S. C. Almo, and J. A. Gerlt. “Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars”, PNAS, 113 (2016) E4161-4169. PMC4961189


T. Long, R. J. Neitz, R. Beasley, C. Kalyanaraman, B. M. Suzuki, M. P. Jacobson, C. Dissous, J. H. McKerrow, D. H. Drewry, W. J. Zuercher, R. Singh, and C. R. Caffrey.  “Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni”,  PLoS Negl. Trop. Dis., 10 (2016) e0004356.  Open Access


J. B. Jameson, A. Kantz, L. Schultz, C. Kalyanaraman, M. P. Jacobson, D. J. Maloney, A. Jadhav, A. Simeonov, and T. R. Holman.  “A high throughput screen identifies potent and selective inhibitors to human epithelial 15-lipoxygenase-2”.  PLoS One, 9 (2014) e104094.  PMC4128814


F. P. Groninger-Poe, J. T. Bouvier, M. W. Vetting, C. Kalyanaraman, R. Kumar, S. C. Almo, M. P. Jacobson, and J. A. Gerlt.  “Evolution of Enzymatic Activities in the Enolase Superfamily:  Galactarate Dehydratase-III from Agrobacterium tumefaciens C58”, Biochemistry 53 (2014) 4192-4203.  Online PMC4081050


R. Kumar, S. Zhao, M. W. Vetting, B. M. Wood, A. Sakai, K. Cho, S. C. Almo, J. V. Sweedler, M. P. Jacobson, J. A. Gerlt, and J. E. Cronan.  “Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine”, mBio, 11 (2014) e00933-13.  PMC3950512


M. Ndao, M. Nath-Chowdhury, M. Sajid, V. Marcus, S. T. Mashiyama, J. Sakanari, E. Chow, Z. Mackey, K. M. Land, M. P. Jacobson, C. Kalyanaraman, J. H. McKerrow, M. J. Arrowood, C. R. Caffrey. “A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection”, Antimicrobial Agents and Chemotherapy, 57 (2013) 6063-6073.  Online  PMC3837922


S. Zhao, R. Kumar, A. Sakai, M. Vetting, B. M. Wood, S. Brown, P. C. Babbitt, S. C. Almo, J. V. Sweedler, J. A. Gerlt, J. E. Cronan, and M. P. Jacobson.  “Discovery of new enzymes and metabolic pathways using structure and genome context”, Nature, 502 (2013) 698-702.  Online  F1000  [News&Views:  M. J. Wargo, “Digging up enzyme functions“, Nature Chemical Biology (2013).]  [Discussed in PSI/Nature Knowledgbase]  PMC3966649


J. W. Choy, C. Bryant, C. M. Calvet, P. S. Doyle, S. S. Gunatilleke, S. S. F. Leung, K. K. H. Ang, S. Chen, J. Gut, J. A. Oses-Prieto, J. B. Johnston, M. R. Arkin, A. L. Burlingame, J. Taunton, M. P. Jacobson, J. M. McKerrow, L. M. Podust, and A. R. Renslo.  “Chemical-Biological Characterization of a Cruzain Inhibitor Reveals a Second Target and a Mammalian Off-Target”.  Beilstein J. Org. Chem, 9 (2013) 15-25.  PMC3566858


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


C. S. Rapp, C. Kalyanaraman, A. Schiffmiller, E. L. Schoenbrun, and M. P. Jacobson.  “A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions:  Relative Binding Affinities in Congeneric Series”, Journal of Chemical Information and Modeling, 51 (2011) 2082-2089.  PMC3183355


J. F. Rakus, C. Kalyanaraman, A. A. Fedorov, Elena V. Fedorov, F. P. Mills-Groninger, K. Bain, J. M. Sauder, S. K. Burley, S. C. Almo, M. P. Jacobson, and J. A. Gerlt. “Computation Facilitated Assignment of Function in the Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase from Oceanobacillus iheyensis”, Biochemistry, 48 (2009) 11546-58.  PMC2787699


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


N. Huang, C. Kalyanaraman, K. Bernacki, and M. P. Jacobson.  “Molecular Mechanics Methods for Predicting Protein-Ligand Binding” (invited feature article), Physical Chemistry Chemical Physics, 8 (2006) 5166–5177.  [PCCP “hot paper”; top downloaded papers in 2006.]  Online


W. Sherman, T. Day, M. P. Jacobson, R. A. Friesner, and R. Farid. “Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects”, Journal of Medicinal Chemistry, 49 (2006) 534–553.  [#3 most cited article in J Med Chem in 2006]  Online


N. Huang, C. Kalyanaraman, J. J. Irwin, and M. P. Jacobson.  “Physics-Based Scoring of Protein-Ligand Complexes:  Enrichment of Known Inhibitors in Large-Scale Virtual Screening”, Journal of Chemical Information and Modeling, 46 (2006) 243–253.  Online


K. Bernacki, C. Kalyanaraman, and M. P. Jacobson.  “Virtual ligand Screening against E. coli Dihydrofolate Reductase:  Improving Docking Enrichment Using Physics-Based Methods” (invited paper), Journal of Biomolecular Screening, 10 (2005) 675–681.  Online