B. X. Tian, C. D. Poulter, and M. P. Jacobson. “Defining the Product Chemical Space of Monoterpenoid Synthases”, PLoS Computational Biology, 12 (2016) e1005053.  PMC4982680



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


M. W. Vetting, N. Al-Obadi, S. Zhao, B. San Francisco, J. Kin, D. W. Wichelecki, J. Bouvier, J. O. Solbiati, H. Vu, X. Zhang, D. Rodionov, J. D. Love, B. S. Hillerich, R. D. Seidel, R. J. Quinn, A. L. Osterman, J. E. Cronan, M. P. Jacobson, J. A. Gerlt, S. C. Almo.   “Experimental Strategies for Functional Annotation and Metabolism Discovery: Targeted Screening of Solute Binding Proteins and Unbiased Panning of Metabolomes”.  Biochemistry, 54 (2015) 909-931.  PMC4310620  C&ENews


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


S. Zhao, A. Sakai, X. Zhang, M. Vetting, R. Kumar, B. Hillerich, B. San Francisco, J. Solbiati, A. Steeves, S. Brown, E. Akiva, A. Barber, R. Seidel, J. E. Cronan, P. C. Babbitt, S. C. Almo, J. A. Gerlt, and M. P. Jacobson.  “Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks”, eLife (2014) e03275.  Online  PMC4113996


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


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


B. Tian, F. Wallrapp, C. Kalyanaraman, S. Zhao, L. A. Eriksson, and M. P. Jacobson.  “Predicting Enzyme-Substrate Specificity with QM/MM Methods: A Case Study of the Stereo-specificity of D-glucarate Dehydratase”.  Biochemistry, 52 (2013) 5511-5513.  Online  PMC3964877


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


J. A. Gerlt, K. N. Allen, S. C. Almo, R. N. Armstrong, P. C. Babbitt, J. E. Cronan, D. Dunaway-Mariano, H. J. Imker, M. P. Jacobson, W. Minor, C. D. Poulter, F. M. Raushel, A. Sali, B. K. Shoichet, and J. V. Sweedler.  “The Enzyme Function Initiative”, Biochemistry, 50 (2011) 9950-9962.  PMC3238057


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


U. Pieper, R. Chiang, J. J. Seffernick, S. D. Brown, M. E. Glasner, L. Kelly, N. Eswar, M. Sauder, S. K. Burley, S. Almo, J. A. Gerlt, F. Raushel, B. K. Shoichet, M. P. Jacobson, P. C. Babbitt, A. Sali.  “Target Selection and Annotation for the Structural Genomics of the Amidohydrolase and Enolase Superfamilies”, Journal of Structural and Functional Genomics, 10 (2009) 107–125.  PMC2693957


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


C. Kalyanaraman, K. Bernacki, and M. P. Jacobson. “Virtual screening against highly charged active sites: Identifying substrates of alpha-beta barrel enzymes”, Biochemistry, 44 (2005) 2059–2071.  [One of top 20 most accessed articles in Biochemistry in 2005.]  Online


V. C. Ruddat, R. Mogul, I. Chorny, C. Chen, N. Perrin, S. Whitman, V. Kenyon, M. P. Jacobson, C. F. Bernasconi, and T. R. Holman. “Tryptophan 500 and Arginine 707 Define Product and Substrate Active Site Binding in Soybean Lipoxygenase-1”, Biochemistry, 43 (2004) 13063–13071.  Online